Multiple platform build/check report for BioC 3.21 - CHECK results for biodbChebi on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4663
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4493
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4504
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4458
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4313
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 kjohnson3

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: 1.13.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz

StartedAt: 2025-02-25 18:55:54 -0500 (Tue, 25 Feb 2025)

EndedAt: 2025-02-25 18:58:13 -0500 (Tue, 25 Feb 2025)

EllapsedTime: 138.7 seconds

RetCode: 0

Status: OK

CheckDir: biodbChebi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.13.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-02-25 18:56:16.438][biodb::testContext]
biodb.INFO [2025-02-25 18:56:16.439][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:56:16.440][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-02-25 18:56:16.440][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:56:16.440][biodb::testContext]
biodb.INFO [2025-02-25 18:56:16.443][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:56:16.444][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-25 18:56:16.447][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:56:16.447][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-25 18:56:16.447][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-25 18:56:16.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.448][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-25 18:56:16.454][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-25 18:56:16.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.455][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-25 18:56:16.455][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-25 18:56:16.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.456][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-25 18:56:16.457][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-25 18:56:16.457][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-25 18:56:16.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.458][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-25 18:56:16.458][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-25 18:56:16.458][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-25 18:56:16.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.459][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-25 18:56:16.459][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-25 18:56:16.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.460][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[2025-02-25 18:56:16.460][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-25 18:56:16.461][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-25 18:56:16.461][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-25 18:56:16.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.462][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-25 18:56:16.462][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-25 18:56:16.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.463][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[2025-02-25 18:56:16.463][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-25 18:56:16.463][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-25 18:56:16.463][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-25 18:56:16.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.464][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:56:16.465][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-25 18:56:16.465][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-25 18:56:16.465][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-25 18:56:16.465][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-25 18:56:16.466][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-25 18:56:16.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.467][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-25 18:56:16.467][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-25 18:56:16.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.468][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-25 18:56:16.468][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-25 18:56:16.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.469][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[2025-02-25 18:56:16.469][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-25 18:56:16.469][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-25 18:56:16.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.470][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-25 18:56:16.470][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-25 18:56:16.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.471][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[2025-02-25 18:56:16.471][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-25 18:56:16.472][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-25 18:56:16.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.473][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:56:16.473][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-25 18:56:16.480][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-25 18:56:16.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.481][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-25 18:56:16.481][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-25 18:56:16.481][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-25 18:56:16.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.484][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-25 18:56:16.495][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.504][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-25 18:56:16.504][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:56:16.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.505][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.506][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.506][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:56:16.506][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:56:16.506][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.507][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-25 18:56:16.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:56:16.507][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:56:16.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.509][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:56:16.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.510][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.510][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:56:16.510][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:56:16.511][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.511][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.511][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-25 18:56:16.512][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.512][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:56:16.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:56:16.513][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.513][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.513][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.514][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.514][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:56:16.514][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:56:16.514][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.515][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-25 18:56:16.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:56:16.515][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:56:16.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.517][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:56:16.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.518][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:56:16.518][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:56:16.519][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.519][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.519][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-25 18:56:16.520][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.520][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-25 18:56:16.520][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.521][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:56:16.521][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.521][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.522][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.522][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:56:16.522][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:56:16.522][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.523][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-25 18:56:16.523][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:56:16.523][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.523][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.524][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.524][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:56:16.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.525][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:56:16.525][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.526][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.526][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.527][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:56:16.527][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:56:16.527][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.527][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.528][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-25 18:56:16.528][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.528][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:56:16.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.529][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:56:16.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.530][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:56:16.530][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:56:16.531][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.531][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-25 18:56:16.531][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:56:16.531][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.531][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.532][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.532][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:56:16.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.533][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:56:16.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.533][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.534][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.534][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:56:16.534][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:56:16.534][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.534][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:56:16.536][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:56:16.536][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.539][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[2025-02-25 18:56:16.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.541][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[2025-02-25 18:56:16.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.543][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[2025-02-25 18:56:16.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.547][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[2025-02-25 18:56:16.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.548][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[2025-02-25 18:56:16.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.551][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[2025-02-25 18:56:16.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.554][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[2025-02-25 18:56:16.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.555][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[2025-02-25 18:56:16.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.557][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-25 18:56:16.558][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-25 18:56:16.559][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-25 18:56:16.559][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-25 18:56:16.559][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:56:16.560][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-25 18:56:16.560][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-25 18:56:16.560][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-25 18:56:16.561][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-25 18:56:16.561][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-25 18:56:16.561][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:56:16.562][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-25 18:56:16.562][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-25 18:56:16.562][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-25 18:56:16.563][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-25 18:56:16.563][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-25 18:56:16.563][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-25 18:56:16.564][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-25 18:56:16.564][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:56:16.564][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-25 18:56:16.565][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-25 18:56:16.565][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-25 18:56:16.565][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-25 18:56:16.566][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-25 18:56:16.566][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-25 18:56:16.566][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-25 18:56:16.567][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-25 18:56:16.567][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-25 18:56:16.567][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-25 18:56:16.568][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-25 18:56:16.568][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-25 18:56:16.569][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-25 18:56:16.569][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-25 18:56:16.569][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-25 18:56:16.570][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-25 18:56:16.570][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-25 18:56:16.570][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-25 18:56:16.571][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-25 18:56:16.571][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-25 18:56:16.571][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-25 18:56:16.572][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-25 18:56:16.572][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-25 18:56:16.572][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-25 18:56:16.573][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-25 18:56:16.573][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-25 18:56:16.573][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-25 18:56:16.574][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-25 18:56:16.574][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-25 18:56:16.575][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-25 18:56:16.575][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-25 18:56:16.575][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-25 18:56:16.576][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-25 18:56:16.576][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-25 18:56:16.576][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-25 18:56:16.577][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-25 18:56:16.577][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-25 18:56:16.577][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-25 18:56:16.578][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-25 18:56:16.578][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-25 18:56:16.578][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-25 18:56:16.579][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-25 18:56:16.579][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-25 18:56:16.579][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-25 18:56:16.580][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-25 18:56:16.580][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-25 18:56:16.581][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-25 18:56:16.581][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:56:16.581][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:56:16.582][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-25 18:56:16.582][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-25 18:56:16.582][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-25 18:56:16.583][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-25 18:56:16.583][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-25 18:56:16.583][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-25 18:56:16.584][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-25 18:56:16.584][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-25 18:56:16.584][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-25 18:56:16.585][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-25 18:56:16.585][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-25 18:56:16.586][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-25 18:56:16.586][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-25 18:56:16.586][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-25 18:56:16.587][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-25 18:56:16.588][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-25 18:56:16.589][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:56:16.590][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:56:16.590][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.591][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.605][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.DEBUG[2025-02-25 18:56:16.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:56:16.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:56:16.621][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-25 18:56:16.624][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-25 18:56:16.625][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.625][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.625][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.626][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:56:16.626][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.626][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.626][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.626][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-25 18:56:16.627][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-25 18:56:16.627][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:56:16.627][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-25 18:56:16.628][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-25 18:56:16.629][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:56:16.629][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:56:16.629][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:56:16.629][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-25 18:56:16.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:56:16.630][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:56:16.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:56:16.630][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:56:16.630][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:56:16.630][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-25 18:56:16.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:56:16.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:56:16.631][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-25 18:56:16.631][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-25 18:56:16.631][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-25 18:56:16.633][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:56:16.634][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:56:16.634][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-25 18:56:16.634][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:56:16.635][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:56:16.635][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:56:16.646][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-25 18:56:16.647][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-25 18:56:16.648][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-25 18:56:16.650][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-25 18:56:16.652][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:56:16.652][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:56:16.653][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-25 18:56:16.653][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-25 18:56:16.672][biodb::testThat]
biodb.INFO [2025-02-25 18:56:16.673][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-25 18:56:16.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:16.673][biodb::testThat]
biodb.TRACE[2025-02-25 18:56:16.675][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-02-25 18:56:16.676][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:56:16.677][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:56:16.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:56:16.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:56:16.690][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.691][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.691][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.697][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.697][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.698][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.706][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.707][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.707][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.708][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.710][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.711][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.712][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.712][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.714][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.714][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.714][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.715][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.716][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:56:16.716][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.716][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.717][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:56:16.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.718][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.718][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.720][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.721][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.722][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:56:16.726][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.726][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.726][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:56:16.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.727][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.728][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.728][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.729][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:56:16.750][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-02-25 18:56:16.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.768][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-25 18:56:16.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-25 18:56:16.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.769][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-25 18:56:16.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-25 18:56:16.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.770][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-25 18:56:16.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-25 18:56:16.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.771][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-25 18:56:16.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-25 18:56:16.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.803][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.804][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.804][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.812][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.815][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.822][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.822][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.823][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.828][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.829][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.830][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.830][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.837][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.837][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.838][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.844][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.845][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.845][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.849][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.850][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.851][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.852][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.852][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.853][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.853][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.859][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.860][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.861][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.862][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.862][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.863][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.863][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.866][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.867][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.868][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.870][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.870][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.870][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.874][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.875][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.876][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.877][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.877][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.878][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.878][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.884][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.885][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.885][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.892][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.892][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.892][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.897][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.897][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.900][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.902][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.902][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.903][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.904][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.904][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.905][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.906][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.907][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.907][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.909][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.910][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.911][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.911][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.912][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.913][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.913][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.914][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.915][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.916][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.916][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.918][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.918][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.918][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.920][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.920][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.921][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.922][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.922][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.923][ef$get] fields variable is a list.
biodb.INFO [2025-02-25 18:56:16.926][biodb::testThat]
biodb.INFO [2025-02-25 18:56:16.926][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-25 18:56:16.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:16.927][biodb::testThat]
biodb.DEBUG[2025-02-25 18:56:16.932][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-02-25 18:56:16.935][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:56:16.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-02-25 18:56:16.937][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:56:16.937][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-02-25 18:56:16.938][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:56:16.945][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:56:16.945][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:56:16.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:56:16.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:56:16.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:56:16.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:56:16.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:56:16.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:56:16.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:56:16.953][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.954][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.954][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.961][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.962][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.962][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.963][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:56:16.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:56:16.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.964][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.964][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.964][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.965][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:56:16.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:56:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.966][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.966][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.967][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:16.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:16.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.968][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.968][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.969][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.970][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.971][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.971][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:56:16.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.972][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:56:16.972][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.973][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.973][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:56:16.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:16.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.974][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.975][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:16.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.976][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.977][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.977][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:16.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:16.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.978][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:56:16.979][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.979][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.980][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:56:16.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:56:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.981][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.981][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.981][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.982][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:56:16.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:56:16.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:56:16.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:56:16.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:56:16.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:56:16.995][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-02-25 18:56:16.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-25 18:56:16.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-25 18:56:16.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-25 18:56:16.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-25 18:56:16.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:16.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-25 18:56:16.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-25 18:56:16.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:16.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-25 18:56:17.001][biodb::testThat]
biodb.INFO [2025-02-25 18:56:17.001][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-25 18:56:17.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:17.002][biodb::testThat]
biodb.TRACE[2025-02-25 18:56:17.003][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:17.003][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:17.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:17.003][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:56:17.004][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-02-25 18:56:17.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:17.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:17.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:17.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:17.014][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:17.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:17.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:17.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:17.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:17.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:17.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:17.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:56:17.017][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-02-25 18:56:17.019][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-25 18:56:17.026][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:56:17.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-25 18:56:17.034][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:56:17.034][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-25 18:56:17.042][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[2025-02-25 18:56:17.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:56:17.044][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:56:17.044][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:56:17.578][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:56:18.075][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:56:18.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-02-25 18:56:18.082][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-02-25 18:56:18.083][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-02-25 18:56:18.088][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:18.089][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:18.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.089][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.090][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.090][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.090][ef$get] fields variable is a list.
biodb.INFO [2025-02-25 18:56:18.092][biodb::testThat]
biodb.INFO [2025-02-25 18:56:18.092][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-25 18:56:18.093][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:18.093][biodb::testThat]
biodb.TRACE[2025-02-25 18:56:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:18.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:18.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:18.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:18.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:18.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:56:18.128][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:56:18.129][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:56:18.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-25 18:56:18.130][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:56:18.130][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-02-25 18:56:18.135][biodb::testThat]
biodb.INFO [2025-02-25 18:56:18.136][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-25 18:56:18.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:18.136][biodb::testThat]
biodb.TRACE[2025-02-25 18:56:18.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:18.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:18.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:18.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:18.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.152][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-25 18:56:18.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-25 18:56:18.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.153][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-25 18:56:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-25 18:56:18.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:18.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:18.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:56:18.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:56:18.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:56:18.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:18.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.166][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.167][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-25 18:56:18.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-25 18:56:18.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-25 18:56:18.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:18.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-25 18:56:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-25 18:56:18.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:18.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-25 18:56:18.174][biodb::testThat]
biodb.INFO [2025-02-25 18:56:18.175][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-25 18:56:18.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:18.175][biodb::testThat]
biodb.INFO [2025-02-25 18:56:18.178][biodb::testThat]
biodb.INFO [2025-02-25 18:56:18.178][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-25 18:56:18.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:18.179][biodb::testThat]
biodb.INFO [2025-02-25 18:56:18.181][biodb::testThat]
biodb.INFO [2025-02-25 18:56:18.182][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-25 18:56:18.182][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:18.182][biodb::testThat]
biodb.DEBUG[2025-02-25 18:56:18.183][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-02-25 18:56:21.743][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-02-25 18:56:57.673][biodb::testThat]
biodb.INFO [2025-02-25 18:56:57.673][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-25 18:56:57.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:57.674][biodb::testThat]
biodb.DEBUG[2025-02-25 18:56:58.081][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[2025-02-25 18:56:58.475][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:58.476][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:58.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:58.476][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:58.477][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:58.477][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:56:58.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:58.478][ef$get] fields variable is a list.
biodb.INFO [2025-02-25 18:56:58.478][biodb::testThat]
biodb.INFO [2025-02-25 18:56:58.479][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-02-25 18:56:58.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:56:58.479][biodb::testThat]
biodb.TRACE[2025-02-25 18:56:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:58.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:58.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:58.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:58.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:56:58.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:56:58.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:58.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:56:58.517][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-02-25 18:56:58.518][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-02-25 18:56:58.523][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:56:58.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:56:58.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:56:59.029][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:56:59.538][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:56:59.548][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-02-25 18:56:59.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-02-25 18:56:59.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:56:59.572][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:56:59.573][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-25 18:56:59.573][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:56:59.573][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-02-25 18:56:59.578][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-25 18:56:59.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-25 18:56:59.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:59.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:59.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:59.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:59.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:59.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:59.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:56:59.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:56:59.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:56:59.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:56:59.591][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:56:59.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:56:59.592][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:56:59.593][private$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[2025-02-25 18:56:59.946][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[2025-02-25 18:57:00.302][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:00.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-02-25 18:57:00.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-02-25 18:57:00.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:00.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:00.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:00.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:00.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:00.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:00.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:00.308][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-02-25 18:57:00.327][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:00.327][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-02-25 18:57:00.328][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:00.328][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:00.328][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:00.329][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:00.329][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:00.329][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:00.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:00.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:00.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:00.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:00.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:00.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:00.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:00.334][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-02-25 18:57:00.334][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:00.335][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:00.335][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-02-25 18:57:00.705][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-02-25 18:57:01.318][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:01.319][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-02-25 18:57:01.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-02-25 18:57:01.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-02-25 18:57:01.322][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:01.322][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:01.323][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:01.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:01.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:01.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:01.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:01.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:01.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:01.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:01.327][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.328][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.328][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.330][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:01.330][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:01.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.330][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.331][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:01.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:01.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.332][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:01.332][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:01.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.333][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:01.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:01.339][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:01.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.340][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:01.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:01.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.341][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:01.342][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:01.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.342][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:01.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:01.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.344][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:01.344][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:01.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.344][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.345][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:01.345][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.345][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.346][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:01.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.347][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:01.347][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:01.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.348][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:01.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:01.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.349][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:01.349][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:01.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.350][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:01.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:01.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.351][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:01.352][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:01.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.352][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.352][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:01.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:01.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.353][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:01.354][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:01.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.354][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:01.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:01.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:01.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:01.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:01.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:01.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:01.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:01.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:01.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:01.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:01.368][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-02-25 18:57:01.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:01.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:01.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:01.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:01.375][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[2025-02-25 18:57:01.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:01.376][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:01.377][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:57:01.730][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:57:02.095][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:02.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-02-25 18:57:02.097][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-02-25 18:57:02.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:02.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:02.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:02.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:02.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:02.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:02.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:02.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:02.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:02.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:02.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:02.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:02.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:02.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:02.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:02.116][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-02-25 18:57:02.116][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:02.117][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-02-25 18:57:02.117][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:02.117][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:02.118][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:02.118][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:02.118][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:02.118][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:02.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:02.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:02.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:02.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:02.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:02.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:02.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:02.127][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-02-25 18:57:02.128][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:02.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:02.128][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-02-25 18:57:02.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-02-25 18:57:02.860][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:02.860][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-02-25 18:57:02.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-02-25 18:57:02.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-02-25 18:57:02.863][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:02.863][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:02.864][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:02.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:02.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:02.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:02.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:02.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:02.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:02.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:02.868][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.868][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.869][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.870][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:02.871][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:02.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.871][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.872][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:02.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:02.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.873][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:02.873][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:02.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.873][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:02.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:02.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.878][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:02.879][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:02.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.879][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:02.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:02.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.881][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:02.881][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:02.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.882][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:02.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:02.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.883][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:02.883][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:02.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.884][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.884][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:02.884][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.885][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.885][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:02.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.886][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:02.886][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:02.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.887][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:02.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:02.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.888][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:02.888][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:02.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.889][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:02.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:02.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.890][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:02.891][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:02.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.891][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.891][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:02.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:02.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.892][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:02.893][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:02.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.893][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:02.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:02.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:02.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:02.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:02.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:02.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:02.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:02.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:02.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:02.919][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-02-25 18:57:02.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:02.929][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:02.930][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:02.931][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-25 18:57:02.931][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:02.932][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-25 18:57:02.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:02.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:02.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:02.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:02.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:02.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:02.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:02.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:02.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:02.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:02.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:02.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:02.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:02.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:02.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:02.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:02.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:02.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:02.943][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-02-25 18:57:02.943][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:02.944][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-02-25 18:57:02.944][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:02.944][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:02.945][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:02.945][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:02.945][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:02.945][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:02.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:02.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:02.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:02.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:02.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:02.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:02.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:02.952][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-02-25 18:57:02.953][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:02.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:02.954][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-02-25 18:57:03.312][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-02-25 18:57:03.673][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:03.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-02-25 18:57:03.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-02-25 18:57:03.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-02-25 18:57:03.677][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:03.677][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:03.678][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:03.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:03.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:03.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:03.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:03.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:03.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:03.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:03.682][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.682][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.683][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.684][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:03.685][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:03.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.685][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.686][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:03.686][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:03.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.686][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.687][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:03.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:03.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.687][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.688][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:03.688][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:03.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.689][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:03.689][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:03.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.690][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.690][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:03.690][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.691][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.691][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:03.691][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:03.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.692][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.692][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:03.692][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:03.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.693][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:03.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:03.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.694][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:03.695][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:03.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.695][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.695][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:03.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:03.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:03.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:03.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.697][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:03.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:03.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:03.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:03.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:03.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:03.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:03.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:03.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:03.713][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-02-25 18:57:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:03.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:03.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:03.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:03.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:03.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:03.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:03.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:03.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:03.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:03.722][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-02-25 18:57:03.722][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:03.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-02-25 18:57:03.723][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:03.723][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:03.724][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:03.724][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:03.724][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:03.724][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:03.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:03.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:03.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:03.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:03.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:03.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:03.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:03.728][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-02-25 18:57:03.729][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:03.729][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:03.730][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-02-25 18:57:04.103][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-02-25 18:57:04.463][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:04.464][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-02-25 18:57:04.469][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-02-25 18:57:04.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-02-25 18:57:04.470][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:04.471][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:04.471][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:04.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:04.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:04.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:04.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:04.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:04.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:04.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:04.476][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.476][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.476][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.478][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:04.478][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:04.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.479][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.479][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:04.479][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:04.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.480][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.480][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:04.480][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:04.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.481][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.481][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:04.481][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:04.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.482][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.482][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:04.482][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:04.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.483][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.483][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:04.484][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.484][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.484][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:04.485][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:04.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.485][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.485][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:04.486][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:04.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.486][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:04.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:04.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.488][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:04.488][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:04.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.489][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.489][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:04.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:04.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.490][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:04.490][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:04.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.491][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:04.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:04.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:04.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:04.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:04.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:04.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:04.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:04.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:04.506][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-02-25 18:57:04.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:04.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:04.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:04.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:04.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:04.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:04.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:04.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:04.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:04.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:04.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:04.515][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-02-25 18:57:04.515][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:04.516][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-02-25 18:57:04.516][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:04.516][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:04.517][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:04.517][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:04.517][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:04.518][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:04.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:04.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:04.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:04.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:04.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:04.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:04.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:04.522][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-02-25 18:57:04.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:04.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:04.523][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-02-25 18:57:04.888][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-02-25 18:57:05.241][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:05.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-02-25 18:57:05.243][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-02-25 18:57:05.244][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-02-25 18:57:05.244][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:05.245][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:05.245][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:05.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:05.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:05.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:05.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:05.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:05.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:05.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:05.253][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.253][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.254][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.256][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:05.256][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:05.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.256][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.257][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:05.257][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:05.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.257][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.258][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:05.258][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:05.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.259][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.259][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:05.259][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:05.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.260][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.260][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:05.260][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:05.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.261][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.261][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:05.261][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.262][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.262][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:05.262][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:05.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.263][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.263][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:05.263][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:05.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.264][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:05.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:05.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:05.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.266][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.267][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:05.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:05.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.268][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:05.268][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:05.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.268][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:05.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:05.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:05.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:05.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:05.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:05.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:05.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:05.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:05.283][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-02-25 18:57:05.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:05.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:05.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:05.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:05.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:05.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:05.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:05.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:05.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:05.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:05.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:05.292][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-02-25 18:57:05.292][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:05.293][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-02-25 18:57:05.293][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:05.293][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:05.294][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:05.294][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:05.294][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:05.295][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:05.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:05.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:05.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:05.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:05.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:05.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:05.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:05.299][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-02-25 18:57:05.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:05.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:05.300][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-02-25 18:57:05.655][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-02-25 18:57:06.030][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:06.031][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-02-25 18:57:06.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-02-25 18:57:06.033][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-02-25 18:57:06.033][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:06.034][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:06.034][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:06.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:06.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:06.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:06.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:06.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:06.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:06.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:06.038][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.043][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.045][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:06.045][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:06.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.045][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:06.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:06.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.047][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:06.047][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:06.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.048][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:06.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:06.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.049][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:06.050][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:06.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.050][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:06.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:06.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.051][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.052][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.052][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.054][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.054][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.054][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.055][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.056][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:06.056][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.056][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.057][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:06.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.058][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.058][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.058][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.060][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:06.060][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:06.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.061][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.061][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:06.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:06.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.062][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:06.062][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:06.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.063][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.063][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:06.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:06.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.064][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:06.064][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:06.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.065][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.065][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:06.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:06.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:06.079][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-02-25 18:57:06.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:06.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:06.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:06.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:06.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:06.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:06.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:06.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:06.086][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-02-25 18:57:06.086][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:06.087][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-02-25 18:57:06.087][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:06.087][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:06.088][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:06.088][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:06.088][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:06.089][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:06.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:06.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:06.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:06.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:06.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:06.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:06.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:06.093][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-02-25 18:57:06.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:06.094][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:06.094][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-02-25 18:57:06.516][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-02-25 18:57:06.913][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:06.914][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-02-25 18:57:06.915][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-02-25 18:57:06.916][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-02-25 18:57:06.916][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:06.917][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:06.920][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:06.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:06.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:06.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:06.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:06.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:06.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:06.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:06.925][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.925][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.926][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.927][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:06.928][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:06.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.928][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.928][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:06.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:06.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.930][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:06.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:06.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.930][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.931][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:06.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:06.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.932][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:06.932][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:06.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.933][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:06.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:06.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.934][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.935][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:06.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.936][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.936][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.937][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.937][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:06.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.938][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:06.938][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.939][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.939][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:06.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.940][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.940][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.941][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:06.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.942][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:06.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:06.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.943][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:06.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:06.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.944][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:06.945][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:06.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.945][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.945][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:06.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:06.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.946][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:06.949][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:06.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.950][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.950][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:06.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:06.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:06.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:06.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:06.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:06.960][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-02-25 18:57:06.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:06.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:06.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:06.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:06.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:06.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:06.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:06.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:06.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:06.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:06.966][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-02-25 18:57:06.967][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:06.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-02-25 18:57:06.967][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:06.968][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:06.968][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:06.968][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:06.968][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:06.969][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:06.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:06.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:06.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:06.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:06.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:06.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:06.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:06.973][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-02-25 18:57:06.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:06.976][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:06.976][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-02-25 18:57:07.394][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-02-25 18:57:07.768][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:07.769][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-02-25 18:57:07.770][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-02-25 18:57:07.771][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-02-25 18:57:07.771][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:07.772][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:07.772][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:07.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:07.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:07.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:07.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:07.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:07.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:07.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:07.777][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.777][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.778][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.779][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:07.779][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:07.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.780][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.780][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:07.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:07.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.781][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:07.782][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:07.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.782][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:07.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:07.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.783][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:07.784][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:07.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.784][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:07.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:07.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.785][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:07.786][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:07.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.786][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:07.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:07.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.788][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:07.788][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:07.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.788][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.789][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:07.789][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.789][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.790][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:07.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.791][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:07.791][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:07.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.792][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:07.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:07.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.793][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:07.793][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:07.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.794][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:07.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:07.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.799][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:07.799][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:07.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.800][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.800][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:07.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:07.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.801][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:07.801][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:07.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.802][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.802][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:07.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:07.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:07.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:07.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:07.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:07.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:07.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:07.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:07.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:07.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:07.814][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-02-25 18:57:07.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:07.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:07.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:07.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:07.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:07.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:07.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:07.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:07.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:07.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:07.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:07.820][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-02-25 18:57:07.821][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:07.821][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-02-25 18:57:07.821][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:07.822][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:07.822][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:07.822][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:07.823][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:07.823][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:07.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:07.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:07.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:07.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:07.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:07.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:07.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:07.830][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-02-25 18:57:07.831][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:07.832][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:07.832][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-02-25 18:57:08.210][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-02-25 18:57:08.576][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:08.577][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-02-25 18:57:08.578][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-02-25 18:57:08.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-02-25 18:57:08.580][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:08.580][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:08.580][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:08.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:08.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:08.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:08.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:08.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:08.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:08.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:08.585][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.586][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.586][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.588][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:08.588][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:08.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.588][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.589][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:08.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:08.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.590][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:08.590][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:08.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.591][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:08.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:08.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.592][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:08.592][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:08.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.593][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:08.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:08.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.594][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:08.595][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:08.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.595][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:08.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.597][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:08.597][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:08.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.597][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.598][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:08.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.598][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.599][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.600][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:08.600][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:08.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.603][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:08.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:08.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.606][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:08.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:08.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.607][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:08.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:08.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.608][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:08.609][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:08.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.609][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:08.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:08.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.611][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:08.611][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:08.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.611][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.612][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:08.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:08.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:08.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:08.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:08.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:08.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:08.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:08.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:08.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:08.623][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-02-25 18:57:08.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:08.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:08.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:08.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:08.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:08.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:08.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:08.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:08.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:08.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:08.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:08.630][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-02-25 18:57:08.630][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:08.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-02-25 18:57:08.633][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:08.634][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:08.634][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:08.634][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:08.635][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:08.635][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:08.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:08.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:08.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:08.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:08.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:08.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:08.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:08.639][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-02-25 18:57:08.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:08.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:08.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-02-25 18:57:08.999][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-02-25 18:57:09.364][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:09.365][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-02-25 18:57:09.366][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-02-25 18:57:09.367][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-02-25 18:57:09.368][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:09.368][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:09.369][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:09.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:09.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:09.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:09.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:09.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:09.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:09.372][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.TRACE[2025-02-25 18:57:09.373][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.373][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.374][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.375][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:09.376][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:09.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.376][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.377][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:09.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.378][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:09.378][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:09.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.378][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:09.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.380][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:09.380][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:09.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.380][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:09.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:09.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.382][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:09.383][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:09.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.383][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:09.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.384][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:09.385][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:09.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.387][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.389][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:09.389][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.390][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.390][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:09.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.391][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:09.391][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:09.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.392][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:09.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:09.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.393][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:09.393][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:09.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.394][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:09.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:09.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.395][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:09.395][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:09.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.396][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.396][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:09.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:09.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.397][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:09.397][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:09.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.398][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.398][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:09.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:09.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:09.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:09.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:09.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:09.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:09.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:09.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:09.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:09.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:09.409][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-02-25 18:57:09.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:09.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:09.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:09.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:09.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:09.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:09.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:09.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:09.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:09.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:09.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:09.418][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-02-25 18:57:09.418][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:09.419][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-02-25 18:57:09.419][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:09.419][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:09.420][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:09.420][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:09.420][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:09.420][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:09.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:09.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:09.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:09.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:09.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:09.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:09.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:09.425][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-02-25 18:57:09.425][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:09.426][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:09.426][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-02-25 18:57:09.788][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-02-25 18:57:10.161][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:10.162][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-02-25 18:57:10.163][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-02-25 18:57:10.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-02-25 18:57:10.164][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:10.164][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:10.165][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:10.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:10.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:10.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:10.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:10.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:10.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:10.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:10.169][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.170][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.170][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.172][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:10.172][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:10.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.172][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.173][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:10.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:10.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.174][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:10.174][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:10.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.175][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:10.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:10.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.176][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:10.176][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:10.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.177][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:10.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:10.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.182][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.182][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.183][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.184][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:10.185][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:10.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.185][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.186][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:10.186][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.187][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.187][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:10.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.189][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.189][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.189][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.191][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:10.191][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:10.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.192][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:10.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:10.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.193][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:10.194][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:10.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.194][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.194][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:10.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.195][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:10.196][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:10.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.196][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.197][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:10.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:10.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:10.211][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-02-25 18:57:10.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:10.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:10.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:10.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:10.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:10.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:10.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:10.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:10.219][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-02-25 18:57:10.219][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:10.220][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-02-25 18:57:10.220][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:10.221][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:10.221][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:10.221][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:10.222][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:10.222][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:10.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:10.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:10.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:10.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:10.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:10.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:10.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:10.226][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-02-25 18:57:10.227][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:10.227][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:10.228][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-02-25 18:57:10.585][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-02-25 18:57:10.954][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:10.955][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-02-25 18:57:10.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-02-25 18:57:10.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-02-25 18:57:10.958][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:10.959][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:10.959][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:10.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:10.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:10.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:10.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:10.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:10.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:10.963][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.TRACE[2025-02-25 18:57:10.964][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.964][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.965][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.967][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:10.967][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:10.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.968][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.968][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:10.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:10.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.970][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:10.970][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:10.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.975][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.975][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:10.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:10.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.977][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:10.977][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:10.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.978][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:10.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:10.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.979][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.980][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.980][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:10.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.982][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:10.982][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:10.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.983][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.983][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:10.983][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.984][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.984][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:10.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:10.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.985][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.986][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.986][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:10.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.988][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:10.988][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:10.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.989][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:10.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:10.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.991][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:10.991][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:10.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.991][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.992][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:10.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:10.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.993][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:10.993][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:10.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.994][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.994][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:10.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:10.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:10.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:10.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:10.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:10.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:11.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:11.011][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-02-25 18:57:11.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:11.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:11.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:11.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:11.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:11.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:11.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:11.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:11.020][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-02-25 18:57:11.020][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:11.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-02-25 18:57:11.021][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:11.021][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:11.022][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:11.022][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:11.022][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:11.022][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:11.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:11.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:11.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:11.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:11.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:11.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:11.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:11.027][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-02-25 18:57:11.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:11.028][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:11.029][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-02-25 18:57:11.397][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-02-25 18:57:11.755][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:11.755][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-02-25 18:57:11.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-02-25 18:57:11.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-02-25 18:57:11.758][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:11.758][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:11.758][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:11.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:11.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:11.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:11.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:11.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:11.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:11.762][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[2025-02-25 18:57:11.763][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.763][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.763][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.768][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:11.769][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:11.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.770][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.770][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:11.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:11.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.771][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:11.771][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:11.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.772][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:11.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:11.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.773][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:11.774][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:11.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.774][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.775][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:11.775][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:11.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.775][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.776][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:11.776][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:11.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.776][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.777][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:11.777][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.778][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.778][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:11.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.779][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:11.779][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:11.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.780][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:11.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:11.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.781][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:11.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:11.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.782][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:11.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:11.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.784][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:11.784][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:11.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.784][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.785][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:11.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.786][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:11.786][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:11.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.787][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:11.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:11.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:11.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:11.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:11.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:11.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:11.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:11.801][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-02-25 18:57:11.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:11.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:11.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:11.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:11.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:11.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:11.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:11.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:11.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:11.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:11.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:11.808][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-02-25 18:57:11.808][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:11.809][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-02-25 18:57:11.809][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:11.810][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:11.810][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:11.810][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:11.810][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:11.811][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:11.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:11.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:11.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:11.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:11.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:11.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:11.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:11.815][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-02-25 18:57:11.816][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:11.816][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:11.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-02-25 18:57:12.175][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-02-25 18:57:12.526][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:12.527][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-02-25 18:57:12.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-02-25 18:57:12.529][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-02-25 18:57:12.529][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:12.530][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:12.530][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:12.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:12.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:12.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:12.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:12.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:12.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:12.534][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.TRACE[2025-02-25 18:57:12.535][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.535][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.536][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.540][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:12.541][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:12.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.542][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.542][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:12.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:12.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.543][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:12.544][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:12.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.544][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:12.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:12.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.546][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:12.546][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:12.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.547][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.547][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:12.547][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:12.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.548][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.548][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:12.548][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:12.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.549][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.549][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:12.550][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.550][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.550][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:12.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.551][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:12.552][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:12.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.552][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:12.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:12.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.554][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:12.554][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:12.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.555][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:12.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:12.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.556][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:12.556][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:12.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.557][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.557][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:12.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:12.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.558][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:12.558][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:12.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.559][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:12.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:12.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:12.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:12.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:12.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:12.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:12.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:12.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:12.572][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-02-25 18:57:12.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:12.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:12.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:12.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:12.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:12.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:12.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:12.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:12.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:12.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:12.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:12.580][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-02-25 18:57:12.580][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:12.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-02-25 18:57:12.581][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:12.581][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:12.581][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:12.582][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:12.582][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:12.582][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:12.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:12.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:12.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:12.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:12.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:12.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:12.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:12.586][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-02-25 18:57:12.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:12.588][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:12.588][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-02-25 18:57:12.948][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-02-25 18:57:13.322][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:13.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-02-25 18:57:13.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-02-25 18:57:13.325][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-02-25 18:57:13.325][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:13.326][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:13.326][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:13.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:13.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:13.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:13.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:13.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:13.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:13.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:13.331][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.331][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.331][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.333][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:13.335][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:13.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.337][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:13.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:13.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.339][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:13.339][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:13.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.340][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.340][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:13.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:13.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.341][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:13.341][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:13.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.342][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:13.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:13.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.343][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:13.343][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:13.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.344][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:13.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:13.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.345][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:13.345][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:13.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.346][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.346][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:13.346][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.347][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.347][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:13.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.348][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:13.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:13.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.349][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:13.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:13.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.350][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:13.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:13.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.351][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:13.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:13.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.353][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:13.353][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:13.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.353][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.354][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:13.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:13.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.355][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:13.355][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:13.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.355][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.356][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:13.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:13.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:13.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:13.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:13.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:13.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:13.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:13.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:13.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:13.369][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-02-25 18:57:13.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:13.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:13.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:13.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:13.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:13.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:13.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:13.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:13.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:13.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:13.376][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-02-25 18:57:13.376][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:13.377][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-02-25 18:57:13.377][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:13.377][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:13.378][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:13.378][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:13.378][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:13.378][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:13.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:13.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:13.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:13.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:13.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:13.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:13.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:13.383][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-02-25 18:57:13.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:13.384][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:13.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-02-25 18:57:13.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-02-25 18:57:14.133][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:14.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-02-25 18:57:14.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-02-25 18:57:14.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-02-25 18:57:14.137][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:14.137][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:14.138][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:14.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:14.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:14.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:14.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:14.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:14.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:14.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:14.146][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.147][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.147][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.149][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:14.149][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:14.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.149][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.150][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:14.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:14.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.151][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:14.151][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:14.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.152][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.152][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:14.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.153][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:14.153][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:14.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.154][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:14.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:14.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.155][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.155][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.156][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.157][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:14.157][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:14.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.158][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.158][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:14.159][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.159][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.159][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:14.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.160][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.161][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.161][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.163][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:14.163][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:14.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.163][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:14.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:14.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.165][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:14.165][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:14.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.165][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.166][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:14.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:14.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.167][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:14.167][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:14.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.168][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.168][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:14.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:14.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:14.182][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-02-25 18:57:14.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:14.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:14.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:14.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:14.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:14.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:14.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:14.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:14.189][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-02-25 18:57:14.189][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:14.190][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-02-25 18:57:14.190][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:14.190][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:14.191][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:14.191][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:14.191][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:14.192][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:14.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:14.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:14.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:14.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:14.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:14.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:14.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:14.196][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-02-25 18:57:14.197][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:14.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:14.197][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-02-25 18:57:14.563][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-02-25 18:57:14.929][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:14.930][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-02-25 18:57:14.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-02-25 18:57:14.933][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-02-25 18:57:14.936][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:14.937][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:14.938][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:14.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:14.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:14.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:14.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:14.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:14.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:14.942][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[2025-02-25 18:57:14.943][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.943][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.943][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.945][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:14.945][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:14.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.946][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.946][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:14.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:14.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.947][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:14.948][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:14.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.948][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.949][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:14.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:14.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.950][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:14.950][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:14.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.951][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:14.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.952][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.953][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.953][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:14.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:14.955][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:14.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.955][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.956][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:14.956][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.956][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.957][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:14.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.958][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.958][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.959][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:14.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.960][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:14.960][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:14.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.961][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:14.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:14.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.962][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:14.963][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:14.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.963][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.964][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:14.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:14.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.965][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:14.965][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:14.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.968][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:14.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:14.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:14.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:14.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:14.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:14.982][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-02-25 18:57:14.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:14.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:14.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:14.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:14.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:14.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:14.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:14.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:14.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:14.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:14.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:14.990][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-02-25 18:57:14.990][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:14.990][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-02-25 18:57:14.991][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:14.991][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:14.991][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:14.992][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:14.992][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:14.992][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:14.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:14.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:14.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:14.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:14.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:14.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:14.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:14.997][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-02-25 18:57:14.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:14.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:15.001][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-02-25 18:57:15.368][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-02-25 18:57:15.754][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:15.755][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-02-25 18:57:15.756][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-02-25 18:57:15.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-02-25 18:57:15.758][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:15.758][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:15.758][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:15.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:15.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:15.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:15.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:15.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:15.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:15.762][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[2025-02-25 18:57:15.763][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.763][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.764][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.765][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:15.765][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:15.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.766][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.766][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:15.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.768][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:15.768][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:15.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.769][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:15.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:15.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.771][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:15.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:15.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.771][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:15.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:15.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.773][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:15.773][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:15.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.774][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:15.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:15.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.775][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:15.775][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:15.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.776][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.776][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:15.777][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.777][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.777][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:15.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.778][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:15.779][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:15.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.779][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:15.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:15.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.781][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:15.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:15.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.781][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:15.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.787][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:15.787][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:15.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.788][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.788][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.789][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:15.790][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:15.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.790][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.790][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:15.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:15.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:15.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:15.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:15.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:15.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:15.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:15.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:15.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:15.802][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-02-25 18:57:15.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:15.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:15.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:15.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:15.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:15.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:15.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:15.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:15.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:15.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:15.809][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-02-25 18:57:15.809][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:15.810][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-02-25 18:57:15.810][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:15.810][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:15.811][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:15.811][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:15.811][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:15.811][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:15.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:15.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:15.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:15.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:15.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:15.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:15.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:15.819][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-02-25 18:57:15.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:15.821][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:15.821][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-02-25 18:57:16.185][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-02-25 18:57:16.550][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:16.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-02-25 18:57:16.552][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-02-25 18:57:16.553][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-02-25 18:57:16.553][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:16.553][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:16.554][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:16.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:16.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:16.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:16.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:16.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:16.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:16.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:16.559][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.559][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.559][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.561][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:16.561][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:16.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.562][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.562][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:16.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:16.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.563][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:16.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:16.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.564][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:16.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:16.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.565][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:16.566][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:16.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.566][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:16.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:16.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.567][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:16.568][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:16.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.568][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:16.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:16.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.570][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:16.570][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:16.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.570][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.571][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:16.571][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.571][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.572][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:16.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.575][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:16.577][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:16.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.578][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:16.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:16.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.579][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:16.579][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:16.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.580][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:16.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:16.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.581][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:16.582][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:16.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.582][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.583][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:16.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:16.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.584][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:16.584][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:16.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.584][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.585][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:16.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:16.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:16.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:16.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:16.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:16.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:16.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:16.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:16.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:16.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:16.596][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-02-25 18:57:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:16.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:16.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:16.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:16.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:16.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:16.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:16.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:16.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:16.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:16.606][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-02-25 18:57:16.606][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:16.607][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-02-25 18:57:16.607][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:16.607][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:16.608][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:16.608][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:16.608][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:16.608][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:16.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:16.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:16.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:16.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:16.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:16.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:16.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:16.613][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-02-25 18:57:16.614][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:16.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:16.614][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-02-25 18:57:17.007][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-02-25 18:57:17.376][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:17.377][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-02-25 18:57:17.379][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-02-25 18:57:17.380][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-02-25 18:57:17.380][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:17.381][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:17.381][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:17.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:17.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:17.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:17.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:17.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:17.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:17.385][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.TRACE[2025-02-25 18:57:17.386][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.386][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.398][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.399][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:17.400][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:17.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.400][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.400][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:17.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:17.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.402][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:17.402][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:17.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.402][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:17.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.404][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:17.404][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:17.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.405][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:17.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:17.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.406][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:17.406][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:17.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.407][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:17.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:17.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.412][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:17.413][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:17.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.413][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.414][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:17.414][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.415][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.415][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:17.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:17.416][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:17.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.417][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:17.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:17.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.418][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:17.419][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:17.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.419][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:17.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:17.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.421][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:17.421][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:17.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.421][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.422][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:17.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:17.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.423][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:17.423][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:17.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.424][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.424][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:17.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:17.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:17.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:17.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:17.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:17.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:17.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:17.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:17.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:17.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:17.436][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-02-25 18:57:17.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:17.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:17.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:17.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:17.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:17.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:17.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:17.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:17.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:17.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:17.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:17.447][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-02-25 18:57:17.447][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:17.448][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-02-25 18:57:17.448][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:17.449][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:17.449][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:17.449][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:17.450][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:17.450][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:17.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:17.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:17.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:17.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:17.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:17.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:17.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:17.454][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-02-25 18:57:17.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:17.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:17.456][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-02-25 18:57:17.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-02-25 18:57:18.171][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:18.172][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-02-25 18:57:18.173][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-02-25 18:57:18.174][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-02-25 18:57:18.174][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:18.175][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:18.175][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:18.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.180][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.180][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.181][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.182][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:18.182][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:18.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.183][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:18.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:18.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.185][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:18.185][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:18.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.186][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.186][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.191][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:18.192][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:18.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.193][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:18.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.194][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:18.195][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:18.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.195][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:18.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:18.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.197][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:18.197][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:18.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.198][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.198][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:18.199][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.199][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.200][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:18.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.201][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.202][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.203][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:18.204][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:18.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.204][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:18.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:18.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.206][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:18.206][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:18.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.207][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.207][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:18.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:18.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.208][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:18.208][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:18.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.209][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:18.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:18.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:18.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:18.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:18.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:18.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:18.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:18.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:18.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.226][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-02-25 18:57:18.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.236][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:18.237][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:18.238][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-25 18:57:18.238][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:18.239][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-25 18:57:18.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:18.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:18.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:18.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:18.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:18.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:18.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:18.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:18.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:18.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:18.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:18.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:18.524][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:18.525][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:18.525][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:18.526][private$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[2025-02-25 18:57:18.920][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[2025-02-25 18:57:19.280][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:19.281][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-02-25 18:57:19.282][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-02-25 18:57:19.284][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[2025-02-25 18:57:19.285][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:19.285][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:19.286][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:57:19.645][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:57:19.997][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:19.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-02-25 18:57:19.999][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-02-25 18:57:20.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:20.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:20.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:20.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:20.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:20.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:20.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:20.004][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-02-25 18:57:20.005][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:20.006][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-02-25 18:57:20.006][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:20.007][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:20.007][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:20.007][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:20.008][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:20.008][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:20.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:20.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:20.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:20.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:20.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:20.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:20.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:20.013][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-02-25 18:57:20.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:20.014][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:20.014][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-02-25 18:57:20.390][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-02-25 18:57:20.774][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:20.775][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-02-25 18:57:20.776][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-02-25 18:57:20.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-02-25 18:57:20.778][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:20.778][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:20.779][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:20.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:20.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:20.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:20.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:20.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:20.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:20.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:20.783][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.784][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.784][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.786][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:20.786][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:20.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.786][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:20.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:20.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.788][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:20.788][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:20.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.789][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:20.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:20.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.790][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:20.790][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:20.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.791][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:20.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:20.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.792][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:20.793][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:20.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.793][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:20.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:20.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.795][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:20.795][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:20.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.795][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.796][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:20.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:20.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.797][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:20.797][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:20.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.798][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.798][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:20.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.799][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.799][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.800][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.801][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:20.802][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:20.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.802][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:20.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.804][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:20.804][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:20.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.805][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.805][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:20.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:20.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.806][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:20.807][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:20.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.807][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:20.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:20.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:20.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:20.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:20.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:20.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:20.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:20.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:20.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:20.820][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-02-25 18:57:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:20.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:20.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:20.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:20.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:20.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:20.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:20.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:20.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:20.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:20.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:20.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:20.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:20.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:20.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:20.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:20.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:20.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:20.835][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-02-25 18:57:20.835][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:20.836][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-02-25 18:57:20.836][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:20.837][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:20.837][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:20.837][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:20.838][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:20.838][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:20.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:20.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:20.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:20.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:20.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:20.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:20.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:20.843][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-02-25 18:57:20.844][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:20.844][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:20.844][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-02-25 18:57:21.218][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-02-25 18:57:21.577][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:21.578][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-02-25 18:57:21.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-02-25 18:57:21.580][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-02-25 18:57:21.580][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:21.581][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:21.581][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:21.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.591][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.591][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.591][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.593][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:21.593][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:21.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.593][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.594][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:21.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:21.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.595][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:21.595][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:21.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.595][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:21.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:21.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.597][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:21.597][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:21.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.597][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:21.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:21.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.598][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:21.599][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:21.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.599][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:21.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:21.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.600][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:21.601][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:21.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.601][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.601][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:21.602][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.602][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.602][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:21.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.604][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.605][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:21.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:21.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.606][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:21.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:21.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.607][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:21.607][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:21.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.608][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.608][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:21.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:21.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.609][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:21.609][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:21.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.610][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.610][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:21.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:21.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:21.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:21.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.620][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-02-25 18:57:21.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.629][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:21.630][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:21.631][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-25 18:57:21.631][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:21.631][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-25 18:57:21.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.755][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:21.756][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:21.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-02-25 18:57:21.757][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:21.757][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-02-25 18:57:21.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.884][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:21.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:21.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-25 18:57:21.887][biodb::testThat]
biodb.INFO [2025-02-25 18:57:21.887][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-02-25 18:57:21.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:21.888][biodb::testThat]
biodb.TRACE[2025-02-25 18:57:21.889][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-25 18:57:21.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-25 18:57:21.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:21.899][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:21.900][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:21.900][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-25 18:57:21.901][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:21.901][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-25 18:57:21.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.908][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:21.909][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:21.910][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-25 18:57:21.910][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:21.910][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-25 18:57:21.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:21.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.923][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-25 18:57:21.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.929][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.930][private$selectFields]
biodb.TRACE[2025-02-25 18:57:21.930][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:21.930][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:21.930][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.931][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.931][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.932][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.932][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.933][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.933][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.933][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.933][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.934][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.934][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:21.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.940][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-25 18:57:21.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.944][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[2025-02-25 18:57:21.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.946][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.946][private$selectFields]
biodb.TRACE[2025-02-25 18:57:21.946][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:21.947][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:21.947][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.947][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.947][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.948][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.948][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.948][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.949][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.949][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.949][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.950][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.950][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.950][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.951][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:21.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.954][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-25 18:57:21.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:21.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.959][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.960][private$selectFields]
biodb.TRACE[2025-02-25 18:57:21.962][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:21.962][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:21.963][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.963][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.963][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.964][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.964][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.964][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.965][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.965][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.965][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:21.965][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.966][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.966][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.966][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:21.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:21.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.970][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-25 18:57:21.970][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-25 18:57:21.970][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-25 18:57:21.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:21.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:21.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:21.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:21.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:21.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:21.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:21.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:21.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:21.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:21.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:21.998][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:21.999][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:21.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:22.000][private$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[2025-02-25 18:57:22.361][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[2025-02-25 18:57:22.713][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:22.713][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-02-25 18:57:22.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-02-25 18:57:22.716][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[2025-02-25 18:57:22.717][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:22.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:22.718][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:57:24.071][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:57:24.428][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:24.429][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-02-25 18:57:24.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-02-25 18:57:24.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.459][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-25 18:57:24.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.474][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.474][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.474][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.475][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.475][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.476][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.476][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.476][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.477][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.477][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.477][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.477][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.478][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.478][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.482][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-25 18:57:24.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.503][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.503][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.504][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.505][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.505][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.506][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.506][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.509][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.510][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.511][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.514][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-25 18:57:24.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.520][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.521][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.521][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.521][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.521][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.522][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.522][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.522][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.523][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.523][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.524][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.524][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.524][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.525][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.525][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.525][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.529][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-25 18:57:24.529][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-25 18:57:24.530][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-25 18:57:24.533][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:24.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:24.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-25 18:57:24.535][biodb::testThat]
biodb.INFO [2025-02-25 18:57:24.535][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-02-25 18:57:24.536][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:24.536][biodb::testThat]
biodb.TRACE[2025-02-25 18:57:24.537][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-25 18:57:24.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-25 18:57:24.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:24.546][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.547][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-25 18:57:24.548][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.549][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-25 18:57:24.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.556][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.557][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.557][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-25 18:57:24.558][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.558][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-25 18:57:24.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.572][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-25 18:57:24.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.577][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.578][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.578][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.578][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.578][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.579][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.579][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.579][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.580][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.580][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.580][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.581][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.581][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.581][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.581][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.582][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.582][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.586][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-25 18:57:24.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.594][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.594][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.594][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.595][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.595][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.595][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.595][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.596][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.596][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.596][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.597][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.597][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.597][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.597][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.598][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.598][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.598][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-25 18:57:24.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.608][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.608][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.609][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.609][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.609][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.610][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.610][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.610][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.611][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.611][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.611][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.612][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.613][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.616][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-25 18:57:24.616][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-25 18:57:24.617][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-25 18:57:24.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:24.648][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.649][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.649][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-25 18:57:24.649][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.650][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-25 18:57:24.651][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.652][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-25 18:57:24.652][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.653][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-25 18:57:24.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.676][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-25 18:57:24.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.682][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.682][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.682][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.682][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.682][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.683][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.683][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.683][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.684][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.684][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.684][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.685][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.685][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.686][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.686][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.690][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-25 18:57:24.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.696][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.696][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.696][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.696][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.697][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.697][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.698][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.698][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.698][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.699][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.699][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.699][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.700][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.700][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.700][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.704][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-25 18:57:24.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.709][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.710][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.710][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.710][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.713][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.713][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.713][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.714][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.714][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.714][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.715][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.715][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.715][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.716][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.716][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.717][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.720][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-25 18:57:24.720][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-25 18:57:24.720][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-25 18:57:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:24.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:24.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-25 18:57:24.726][biodb::testThat]
biodb.INFO [2025-02-25 18:57:24.726][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-02-25 18:57:24.726][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:24.727][biodb::testThat]
biodb.TRACE[2025-02-25 18:57:24.728][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-25 18:57:24.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-25 18:57:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:24.738][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.739][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-02-25 18:57:24.740][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.740][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-02-25 18:57:24.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.748][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.749][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-02-25 18:57:24.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.750][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-02-25 18:57:24.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:24.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.764][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-25 18:57:24.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.770][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.770][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.771][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.771][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.771][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.771][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.772][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.772][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.773][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.773][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.773][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.774][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.774][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.775][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.778][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-02-25 18:57:24.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.785][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.785][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.785][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.785][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.786][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.786][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.786][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.787][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.787][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.787][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.788][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.788][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.788][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.789][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.789][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.789][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.790][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.793][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-25 18:57:24.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.799][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.800][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.800][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.800][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.800][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.801][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.801][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.802][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.802][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.802][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.803][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.803][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.803][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.803][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.804][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.804][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.808][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-02-25 18:57:24.808][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-25 18:57:24.808][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-25 18:57:24.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:24.831][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.832][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-02-25 18:57:24.833][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.833][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-02-25 18:57:24.834][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:24.835][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:57:24.836][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-02-25 18:57:24.836][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:57:24.836][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-02-25 18:57:24.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:24.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:24.856][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-02-25 18:57:24.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.863][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.863][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.863][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.863][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.864][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.864][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.865][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.865][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.865][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.866][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.866][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.866][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.867][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.867][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.871][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-02-25 18:57:24.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.877][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.877][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.877][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.877][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.878][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.878][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.878][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.879][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.879][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.879][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.880][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.880][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.880][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.880][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.881][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.881][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.885][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-02-25 18:57:24.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:24.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.891][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.891][private$selectFields]
biodb.TRACE[2025-02-25 18:57:24.891][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-02-25 18:57:24.891][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-02-25 18:57:24.892][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.892][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.892][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.893][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.893][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.893][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.894][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.894][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.894][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-02-25 18:57:24.894][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.895][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.895][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.895][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-02-25 18:57:24.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:24.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:24.899][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-02-25 18:57:24.899][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-02-25 18:57:24.899][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-02-25 18:57:24.906][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:24.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-02-25 18:57:24.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:24.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-25 18:57:24.908][biodb::testThat]
biodb.INFO [2025-02-25 18:57:24.909][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-02-25 18:57:24.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:24.909][biodb::testThat]
biodb.DEBUG[2025-02-25 18:57:24.910][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-02-25 18:57:24.910][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:57:24.911][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-02-25 18:57:24.911][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:57:24.911][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:24.911][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:24.912][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:24.912][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:24.912][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:24.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:24.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:24.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:24.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:24.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:24.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:24.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:24.916][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-02-25 18:57:24.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:24.917][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:24.918][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-02-25 18:57:25.282][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-02-25 18:57:25.647][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:25.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-02-25 18:57:25.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-02-25 18:57:25.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-02-25 18:57:25.651][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:25.651][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:57:25.651][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:25.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:25.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:25.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:25.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:25.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:25.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:25.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:25.656][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.656][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.661][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.662][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:25.663][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:25.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.663][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.664][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:25.664][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:25.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.664][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.665][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:25.665][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:25.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.665][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.666][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:25.666][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:25.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.666][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.667][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:25.667][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:25.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.668][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.668][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:25.668][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:25.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.669][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.669][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:25.669][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:25.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.670][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.670][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:25.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:25.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.671][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.671][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:25.671][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:25.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.672][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.672][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:25.672][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:25.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.673][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:25.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:25.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:25.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:25.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:25.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:25.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:25.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:25.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:25.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:25.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:25.684][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-02-25 18:57:25.684][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-02-25 18:57:25.688][biodb::testThat]
biodb.INFO [2025-02-25 18:57:25.688][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-02-25 18:57:25.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:25.689][biodb::testThat]
biodb.DEBUG[2025-02-25 18:57:25.695][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-02-25 18:57:25.695][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-02-25 18:57:25.695][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-02-25 18:57:25.696][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-02-25 18:57:25.696][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-02-25 18:57:25.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:57:25.697][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:57:25.697][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:25.698][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:57:25.698][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:57:25.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:25.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:25.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:25.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:25.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:25.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:25.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:25.702][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-02-25 18:57:25.703][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:25.704][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:25.704][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-02-25 18:57:26.058][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-02-25 18:57:26.428][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:26.429][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-02-25 18:57:26.430][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-02-25 18:57:26.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:26.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:26.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:26.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:26.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:26.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:26.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:26.435][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-02-25 18:57:26.436][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:26.436][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:26.436][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-02-25 18:57:26.795][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-02-25 18:57:27.159][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:27.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-02-25 18:57:27.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-02-25 18:57:27.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:27.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:27.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:27.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:27.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:27.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:27.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:27.165][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-02-25 18:57:27.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:27.166][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:27.167][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-02-25 18:57:27.532][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-02-25 18:57:27.954][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:27.955][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-02-25 18:57:27.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-02-25 18:57:27.958][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-02-25 18:57:27.960][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:57:27.960][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-02-25 18:57:27.961][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-02-25 18:57:27.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:27.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:27.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:27.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:27.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:27.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:27.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:27.965][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.966][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.966][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.968][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:27.968][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:27.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.968][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.969][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:27.969][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:27.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.970][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.970][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:27.970][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:27.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.971][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:27.971][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:27.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.972][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.972][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:27.972][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:27.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.973][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.973][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:27.974][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:27.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.974][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:27.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:27.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.975][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.975][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:27.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:27.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.976][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.977][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:27.977][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:27.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.977][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.978][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:27.978][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:27.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.978][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:27.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:27.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:27.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:27.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:27.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:27.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:27.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:27.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:27.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:27.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:27.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:27.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:27.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:27.992][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.992][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.992][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:27.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:27.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.994][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:27.994][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:27.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.995][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.995][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:27.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:27.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.996][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:27.996][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:27.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.997][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:27.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:27.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.998][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:27.998][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:27.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:27.999][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:27.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:27.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:28.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.000][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.001][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.001][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.003][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.003][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.003][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.004][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.010][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:28.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:28.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.011][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.012][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:28.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:28.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.013][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.013][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.015][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:28.015][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:28.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.015][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:28.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:28.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.017][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:28.017][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:28.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.018][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.018][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:28.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:28.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.019][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:28.019][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:28.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.020][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:28.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:28.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:28.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:28.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:28.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:28.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:28.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:28.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:28.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:57:28.032][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.033][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.033][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.035][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:28.035][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:28.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.035][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.036][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:57:28.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:57:28.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.037][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:28.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:28.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.038][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:57:28.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:57:28.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.039][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:28.039][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:28.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.040][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:57:28.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:57:28.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.041][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.041][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.042][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:57:28.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.043][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.044][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.044][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.044][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:57:28.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.045][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:28.046][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:28.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.046][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.046][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:57:28.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:57:28.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.048][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.048][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.048][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.050][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:28.050][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:28.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.050][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:28.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:28.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.052][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:28.052][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:28.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.053][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.053][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:57:28.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:57:28.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.054][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:28.054][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:28.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.055][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.055][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:57:28.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:57:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:57:28.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:28.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:57:28.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:57:28.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:28.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:57:28.072][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-02-25 18:57:28.073][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-02-25 18:57:28.073][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-02-25 18:57:28.078][biodb::testThat]
biodb.INFO [2025-02-25 18:57:28.078][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-02-25 18:57:28.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:28.079][biodb::testThat]
biodb.INFO [2025-02-25 18:57:28.087][biodb::testThat]
biodb.INFO [2025-02-25 18:57:28.087][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-02-25 18:57:28.087][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:28.087][biodb::testThat]
biodb.INFO [2025-02-25 18:57:28.090][biodb::testThat]
biodb.INFO [2025-02-25 18:57:28.091][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-02-25 18:57:28.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:28.091][biodb::testThat]
biodb.DEBUG[2025-02-25 18:57:28.092][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:28.093][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:28.093][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:28.094][private$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[2025-02-25 18:57:28.565][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[2025-02-25 18:57:29.064][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:29.065][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-02-25 18:57:29.067][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-02-25 18:57:29.071][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:57:29.071][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:57:29.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:29.072][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:57:29.072][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:29.072][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:57:29.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:57:29.073][ef$get] fields variable is a list.
biodb.INFO [2025-02-25 18:57:29.073][biodb::testThat]
biodb.INFO [2025-02-25 18:57:29.073][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-02-25 18:57:29.074][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:29.074][biodb::testThat]
biodb.ERROR[2025-02-25 18:57:29.078][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-02-25 18:57:29.087][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-02-25 18:57:29.091][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-25 18:57:29.092][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-25 18:57:29.092][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-25 18:57:29.092][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-25 18:57:29.092][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.093][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.093][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.094][FUN] Functions in observer BiodbConfig: [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 [2025-02-25 18:57:29.097][biodb::testContext]
biodb.INFO [2025-02-25 18:57:29.097][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:57:29.097][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-02-25 18:57:29.098][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:57:29.098][biodb::testContext]
biodb.INFO [2025-02-25 18:57:29.098][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:57:29.099][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-25 18:57:29.100][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:57:29.101][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-25 18:57:29.101][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-25 18:57:29.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.102][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-25 18:57:29.102][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-25 18:57:29.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.103][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-25 18:57:29.103][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-25 18:57:29.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.104][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-25 18:57:29.105][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-25 18:57:29.105][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-25 18:57:29.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.106][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-25 18:57:29.106][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-25 18:57:29.106][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-25 18:57:29.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.107][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-25 18:57:29.107][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-25 18:57:29.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.108][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-25 18:57:29.109][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-25 18:57:29.109][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-25 18:57:29.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.110][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-25 18:57:29.110][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-25 18:57:29.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.111][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-25 18:57:29.111][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-25 18:57:29.112][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-25 18:57:29.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.112][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:57:29.113][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-25 18:57:29.113][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-25 18:57:29.113][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-25 18:57:29.113][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-25 18:57:29.114][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-25 18:57:29.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.115][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-25 18:57:29.115][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-25 18:57:29.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.116][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-25 18:57:29.116][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-25 18:57:29.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.117][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-25 18:57:29.117][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-25 18:57:29.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.118][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-25 18:57:29.119][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-25 18:57:29.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.119][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-25 18:57:29.120][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-25 18:57:29.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.121][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:57:29.121][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-25 18:57:29.127][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-25 18:57:29.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.128][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-25 18:57:29.129][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-25 18:57:29.129][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-25 18:57:29.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.130][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-25 18:57:29.130][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.131][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-25 18:57:29.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:57:29.132][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.132][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.132][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.133][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:57:29.133][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:57:29.133][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.133][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:57:29.134][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:57:29.135][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:57:29.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.135][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:57:29.136][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.136][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.136][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.137][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:57:29.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:57:29.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.137][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.138][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-25 18:57:29.138][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.139][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:57:29.139][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:57:29.139][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.140][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.140][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.140][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.140][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:57:29.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:57:29.141][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.141][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-25 18:57:29.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:57:29.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:57:29.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:57:29.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.144][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.144][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.144][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:57:29.144][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:57:29.145][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.145][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.145][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-25 18:57:29.146][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.146][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-25 18:57:29.146][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.147][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:57:29.147][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.147][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.148][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:57:29.148][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:57:29.148][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.149][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-25 18:57:29.149][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:57:29.149][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.149][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.149][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.150][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:57:29.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.150][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:57:29.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.151][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.151][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.152][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:57:29.152][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:57:29.152][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.152][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.153][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-25 18:57:29.153][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.153][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:57:29.154][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.154][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:57:29.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.154][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.155][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.155][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.155][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:57:29.155][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:57:29.156][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.156][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-25 18:57:29.156][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:57:29.156][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.157][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.157][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.157][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:57:29.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.158][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:57:29.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.159][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.159][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:57:29.159][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:57:29.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.160][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:57:29.160][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:57:29.160][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.162][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[2025-02-25 18:57:29.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.164][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[2025-02-25 18:57:29.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.166][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[2025-02-25 18:57:29.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.168][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[2025-02-25 18:57:29.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.171][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[2025-02-25 18:57:29.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.175][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[2025-02-25 18:57:29.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.182][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-25 18:57:29.183][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-25 18:57:29.183][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-25 18:57:29.184][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-25 18:57:29.184][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:57:29.184][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-25 18:57:29.185][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-25 18:57:29.185][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-25 18:57:29.185][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-25 18:57:29.186][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-25 18:57:29.186][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:57:29.186][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-25 18:57:29.187][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-25 18:57:29.187][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-25 18:57:29.188][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-25 18:57:29.188][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-25 18:57:29.188][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-25 18:57:29.189][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-25 18:57:29.189][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:57:29.189][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-25 18:57:29.190][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-25 18:57:29.190][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-25 18:57:29.190][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-25 18:57:29.191][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-25 18:57:29.191][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-25 18:57:29.192][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-25 18:57:29.192][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-25 18:57:29.192][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-25 18:57:29.193][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-25 18:57:29.193][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-25 18:57:29.193][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-25 18:57:29.194][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-25 18:57:29.194][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-25 18:57:29.194][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-25 18:57:29.195][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-25 18:57:29.195][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-25 18:57:29.195][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-25 18:57:29.196][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-25 18:57:29.196][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-25 18:57:29.197][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-25 18:57:29.197][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-25 18:57:29.197][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-25 18:57:29.198][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-25 18:57:29.198][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-25 18:57:29.198][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-25 18:57:29.199][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-25 18:57:29.199][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-25 18:57:29.199][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-25 18:57:29.200][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-25 18:57:29.200][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-25 18:57:29.201][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-25 18:57:29.201][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-25 18:57:29.201][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-25 18:57:29.202][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-25 18:57:29.202][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-25 18:57:29.202][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-25 18:57:29.203][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-25 18:57:29.203][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-25 18:57:29.203][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-25 18:57:29.204][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-25 18:57:29.204][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-25 18:57:29.205][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-25 18:57:29.205][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-25 18:57:29.205][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-25 18:57:29.206][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-25 18:57:29.206][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-25 18:57:29.206][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:57:29.207][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:57:29.207][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-25 18:57:29.207][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-25 18:57:29.208][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-25 18:57:29.208][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-25 18:57:29.209][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-25 18:57:29.209][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-25 18:57:29.209][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-25 18:57:29.210][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-25 18:57:29.210][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-25 18:57:29.210][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-25 18:57:29.211][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-25 18:57:29.211][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-25 18:57:29.211][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-25 18:57:29.212][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-25 18:57:29.212][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-25 18:57:29.213][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-25 18:57:29.213][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:57:29.214][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:57:29.214][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.214][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.219][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[2025-02-25 18:57:29.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:57:29.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:29.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:29.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:29.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:29.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:29.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:29.242][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-25 18:57:29.242][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-25 18:57:29.243][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.243][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.243][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.243][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:57:29.244][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.244][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.244][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-25 18:57:29.245][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-25 18:57:29.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:57:29.245][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.245][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-25 18:57:29.246][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-25 18:57:29.247][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:57:29.247][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:57:29.247][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:57:29.247][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-25 18:57:29.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.248][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:57:29.248][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:57:29.248][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:57:29.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:57:29.249][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:57:29.249][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-25 18:57:29.249][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:57:29.249][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:57:29.249][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-25 18:57:29.250][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-25 18:57:29.250][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-25 18:57:29.250][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:57:29.250][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:57:29.251][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-25 18:57:29.251][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:57:29.252][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:57:29.252][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:57:29.253][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-25 18:57:29.253][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-25 18:57:29.254][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-25 18:57:29.254][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-25 18:57:29.254][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:57:29.255][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:57:29.255][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-25 18:57:29.255][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-25 18:57:29.256][biodb::testThat]
biodb.INFO [2025-02-25 18:57:29.256][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-02-25 18:57:29.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:57:29.256][biodb::testThat]
biodb.DEBUG[2025-02-25 18:57:29.258][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-25 18:57:29.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:29.259][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:29.260][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-02-25 18:57:29.594][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-02-25 18:57:30.106][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:30.106][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-02-25 18:57:30.108][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-02-25 18:57:30.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:57:30.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:30.110][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:30.111][private$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[2025-02-25 18:57:30.462][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[2025-02-25 18:57:30.824][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:57:30.825][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-02-25 18:57:30.826][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-02-25 18:57:30.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:57:30.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:57:30.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:57:30.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:57:30.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:57:30.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:57:30.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:57:30.831][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[2025-02-25 18:57:30.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:57:30.836][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:57:30.837][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:58:04.021][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:58:04.392][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:58:04.393][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-02-25 18:58:04.395][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-02-25 18:58:04.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:04.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:04.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:04.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:04.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:04.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:04.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:04.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:04.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:04.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:04.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:04.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:04.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:04.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:04.409][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:58:04.410][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:58:04.411][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-25 18:58:04.411][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:58:04.412][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-25 18:58:04.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:04.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:04.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:04.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:04.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:04.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:04.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:04.416][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:58:04.417][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:58:04.417][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-25 18:58:04.418][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:58:04.418][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-25 18:58:04.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:04.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:04.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:04.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:04.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:04.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:04.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:04.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:04.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:04.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:04.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:04.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:04.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:04.424][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[2025-02-25 18:58:04.426][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:58:04.427][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:58:04.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-02-25 18:58:04.427][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:58:04.428][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-02-25 18:58:04.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:04.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:04.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:04.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:04.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:04.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:04.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:04.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:58:04.437][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:58:04.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-02-25 18:58:04.438][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:58:04.438][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-02-25 18:58:04.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:04.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:04.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:04.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:04.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:04.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:04.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:04.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:58:04.443][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:58:04.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:58:04.444][private$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[2025-02-25 18:58:04.803][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[2025-02-25 18:58:05.158][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:58:05.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-02-25 18:58:05.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-02-25 18:58:05.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:05.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:05.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:05.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:05.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:05.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:05.165][FUN] Functions in observer BiodbConfig: [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 [2025-02-25 18:58:05.167][biodb::testThat]
biodb.INFO [2025-02-25 18:58:05.168][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-02-25 18:58:05.168][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:58:05.168][biodb::testThat]
biodb.DEBUG[2025-02-25 18:58:05.169][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[2025-02-25 18:58:05.171][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:58:05.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:58:05.171][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:58:05.525][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:58:05.890][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:58:05.891][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-02-25 18:58:05.892][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-02-25 18:58:05.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:05.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:05.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:05.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:05.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:05.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:05.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:05.897][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:58:05.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:58:05.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:58:05.899][private$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[2025-02-25 18:58:06.266][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[2025-02-25 18:58:06.627][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:58:06.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-02-25 18:58:06.629][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-02-25 18:58:06.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:06.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-25 18:58:06.634][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-25 18:58:06.635][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-25 18:58:06.635][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-25 18:58:06.635][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-25 18:58:06.636][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.636][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.636][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-25 18:58:06.638][biodb::testContext]
biodb.INFO [2025-02-25 18:58:06.638][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:58:06.639][biodb::testContext] Test context - Test web services
biodb.INFO [2025-02-25 18:58:06.639][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:58:06.639][biodb::testContext]
biodb.INFO [2025-02-25 18:58:06.640][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:58:06.640][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-25 18:58:06.642][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:58:06.642][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-25 18:58:06.642][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-25 18:58:06.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.643][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-25 18:58:06.644][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-25 18:58:06.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.645][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-25 18:58:06.645][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-25 18:58:06.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.646][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-25 18:58:06.646][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-25 18:58:06.646][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-25 18:58:06.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.647][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-25 18:58:06.647][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-25 18:58:06.648][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-25 18:58:06.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.649][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-25 18:58:06.649][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-25 18:58:06.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.650][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-25 18:58:06.650][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-25 18:58:06.650][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-25 18:58:06.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.651][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-25 18:58:06.651][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-25 18:58:06.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.652][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-25 18:58:06.653][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-25 18:58:06.653][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-25 18:58:06.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.654][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:58:06.654][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-25 18:58:06.654][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-25 18:58:06.655][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-25 18:58:06.655][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-25 18:58:06.655][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-25 18:58:06.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.656][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-25 18:58:06.656][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-25 18:58:06.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.657][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-25 18:58:06.657][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-25 18:58:06.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.658][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[2025-02-25 18:58:06.658][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-25 18:58:06.658][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-25 18:58:06.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.659][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-25 18:58:06.660][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-25 18:58:06.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.660][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[2025-02-25 18:58:06.661][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-25 18:58:06.661][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-25 18:58:06.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.662][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:58:06.662][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-25 18:58:06.668][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-25 18:58:06.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.676][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.DEBUG[2025-02-25 18:58:06.676][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-25 18:58:06.676][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-25 18:58:06.677][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-25 18:58:06.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.678][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-25 18:58:06.678][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.678][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-25 18:58:06.679][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.679][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:06.679][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.679][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.680][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.680][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:58:06.680][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:06.681][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.681][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-25 18:58:06.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:06.681][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:06.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.683][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:06.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.684][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.684][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:06.684][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:06.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.685][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.685][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-25 18:58:06.686][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.686][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:58:06.686][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.686][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:06.687][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.687][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.687][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.687][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.688][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:58:06.688][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:06.688][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.688][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-25 18:58:06.688][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:06.689][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.689][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.689][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:58:06.689][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:58:06.689][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:58:06.689][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:58:06.689][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:58:06.690][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:06.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.690][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:06.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.691][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:06.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:06.692][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.692][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.692][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-25 18:58:06.693][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.693][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-25 18:58:06.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.694][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:06.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.694][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.694][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.695][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:58:06.695][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:06.695][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.696][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-25 18:58:06.696][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:06.696][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.696][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.697][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.697][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:06.697][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.697][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:06.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.698][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.699][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:06.699][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:06.699][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.699][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.700][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-25 18:58:06.700][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.700][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:58:06.701][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.701][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:06.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.701][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.702][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.702][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:58:06.702][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:06.703][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.703][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-25 18:58:06.703][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:06.703][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.704][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.704][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.704][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:06.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.705][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:06.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.706][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.706][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.706][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:06.706][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:06.707][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.707][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:06.707][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:58:06.707][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.709][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[2025-02-25 18:58:06.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.712][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[2025-02-25 18:58:06.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.713][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[2025-02-25 18:58:06.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.717][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[2025-02-25 18:58:06.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.718][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[2025-02-25 18:58:06.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.720][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[2025-02-25 18:58:06.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.722][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[2025-02-25 18:58:06.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.723][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[2025-02-25 18:58:06.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.727][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-25 18:58:06.727][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-25 18:58:06.728][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-25 18:58:06.728][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-25 18:58:06.728][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:58:06.729][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-25 18:58:06.729][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-25 18:58:06.729][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-25 18:58:06.730][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-25 18:58:06.730][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-25 18:58:06.731][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:58:06.731][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-25 18:58:06.731][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-25 18:58:06.732][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-25 18:58:06.732][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-25 18:58:06.732][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-25 18:58:06.733][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-25 18:58:06.733][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-25 18:58:06.733][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:58:06.734][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-25 18:58:06.734][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-25 18:58:06.734][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-25 18:58:06.735][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-25 18:58:06.735][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-25 18:58:06.736][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-25 18:58:06.736][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-25 18:58:06.736][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-25 18:58:06.737][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-25 18:58:06.737][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-25 18:58:06.737][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-25 18:58:06.738][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-25 18:58:06.738][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-25 18:58:06.738][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-25 18:58:06.739][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-25 18:58:06.739][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-25 18:58:06.740][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-25 18:58:06.740][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-25 18:58:06.740][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-25 18:58:06.741][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-25 18:58:06.741][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-25 18:58:06.741][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-25 18:58:06.742][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-25 18:58:06.742][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-25 18:58:06.742][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-25 18:58:06.743][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-25 18:58:06.743][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-25 18:58:06.743][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-25 18:58:06.744][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-25 18:58:06.744][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-25 18:58:06.745][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-25 18:58:06.745][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-25 18:58:06.745][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-25 18:58:06.746][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-25 18:58:06.746][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-25 18:58:06.746][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-25 18:58:06.747][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-25 18:58:06.747][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-25 18:58:06.747][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-25 18:58:06.748][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-25 18:58:06.748][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-25 18:58:06.749][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-25 18:58:06.749][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-25 18:58:06.749][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-25 18:58:06.750][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-25 18:58:06.750][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-25 18:58:06.750][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-25 18:58:06.751][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:58:06.751][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:58:06.751][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-25 18:58:06.752][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-25 18:58:06.752][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-25 18:58:06.753][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-25 18:58:06.753][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-25 18:58:06.753][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-25 18:58:06.754][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-25 18:58:06.754][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-25 18:58:06.754][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-25 18:58:06.755][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-25 18:58:06.755][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-25 18:58:06.755][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-25 18:58:06.756][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-25 18:58:06.756][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-25 18:58:06.756][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-25 18:58:06.757][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-25 18:58:06.758][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:58:06.758][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:58:06.758][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.759][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.759][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[2025-02-25 18:58:06.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.765][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[2025-02-25 18:58:06.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.766][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[2025-02-25 18:58:06.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.771][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[2025-02-25 18:58:06.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.775][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.DEBUG[2025-02-25 18:58:06.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.777][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[2025-02-25 18:58:06.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.780][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[2025-02-25 18:58:06.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.783][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[2025-02-25 18:58:06.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.785][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[2025-02-25 18:58:06.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:06.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:06.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:06.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:06.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:06.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:06.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:06.788][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[2025-02-25 18:58:06.789][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-25 18:58:06.789][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-25 18:58:06.790][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.790][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:06.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.791][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.792][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.792][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-25 18:58:06.792][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-25 18:58:06.792][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:06.793][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.793][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-25 18:58:06.793][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:58:06.794][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-25 18:58:06.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.795][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:06.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:06.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:06.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:06.796][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:58:06.796][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-25 18:58:06.796][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:06.797][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:06.797][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:06.797][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-25 18:58:06.797][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-25 18:58:06.798][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:58:06.798][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:58:06.798][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-25 18:58:06.799][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:58:06.799][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:58:06.800][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:58:06.801][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-25 18:58:06.801][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-25 18:58:06.801][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-25 18:58:06.802][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-25 18:58:06.802][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:58:06.802][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:58:06.803][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-25 18:58:06.803][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-25 18:58:06.803][biodb::testThat]
biodb.INFO [2025-02-25 18:58:06.804][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-02-25 18:58:06.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:58:06.804][biodb::testThat]
biodb.DEBUG[2025-02-25 18:58:06.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-25 18:58:06.806][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:58:06.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-25 18:58:06.807][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:58:06.808][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-25 18:58:06.809][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[2025-02-25 18:58:06.810][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:58:06.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:58:06.811][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-02-25 18:58:07.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-02-25 18:58:07.532][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:58:07.533][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-02-25 18:58:07.534][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-02-25 18:58:07.537][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-25 18:58:07.538][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-25 18:58:07.538][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-25 18:58:07.538][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-25 18:58:07.539][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.539][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.539][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-25 18:58:07.541][biodb::testContext]
biodb.INFO [2025-02-25 18:58:07.541][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:58:07.542][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-02-25 18:58:07.542][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-25 18:58:07.542][biodb::testContext]
biodb.INFO [2025-02-25 18:58:07.543][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:58:07.543][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-25 18:58:07.545][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:58:07.546][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-25 18:58:07.546][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-25 18:58:07.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.547][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[2025-02-25 18:58:07.547][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-25 18:58:07.547][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-25 18:58:07.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.548][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-25 18:58:07.549][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-25 18:58:07.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.550][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-25 18:58:07.550][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-25 18:58:07.550][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-25 18:58:07.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.551][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-25 18:58:07.551][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-25 18:58:07.551][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-25 18:58:07.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.552][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-25 18:58:07.553][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-25 18:58:07.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.554][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-25 18:58:07.554][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-25 18:58:07.554][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-25 18:58:07.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.555][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[2025-02-25 18:58:07.555][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-25 18:58:07.555][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-25 18:58:07.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.556][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-25 18:58:07.557][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-25 18:58:07.557][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-25 18:58:07.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.558][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:58:07.558][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-25 18:58:07.558][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-25 18:58:07.559][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-25 18:58:07.559][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-25 18:58:07.559][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-25 18:58:07.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.560][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-25 18:58:07.560][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-25 18:58:07.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.561][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-25 18:58:07.561][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-25 18:58:07.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.562][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-25 18:58:07.563][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-25 18:58:07.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.563][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[2025-02-25 18:58:07.564][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-25 18:58:07.564][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-25 18:58:07.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.565][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-25 18:58:07.565][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-25 18:58:07.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.566][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-25 18:58:07.566][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-25 18:58:07.572][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-25 18:58:07.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.574][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-25 18:58:07.574][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-25 18:58:07.574][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-25 18:58:07.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.575][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-25 18:58:07.576][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.576][self$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[2025-02-25 18:58:07.576][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.576][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:07.577][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.577][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.577][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.577][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.578][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:58:07.578][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:07.578][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.578][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:58:07.579][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:58:07.580][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:07.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:07.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.581][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.581][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.582][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:07.582][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:07.582][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.582][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.583][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-25 18:58:07.583][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.584][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:58:07.586][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.588][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:07.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.589][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.589][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:58:07.590][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:07.590][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.590][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-25 18:58:07.590][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-25 18:58:07.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:07.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.592][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:07.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.593][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.593][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.593][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:07.593][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:07.594][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.594][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.594][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-25 18:58:07.595][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.595][self$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[2025-02-25 18:58:07.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.596][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:07.596][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.596][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.596][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.597][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.597][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-25 18:58:07.597][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:07.597][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.598][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-25 18:58:07.598][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:07.598][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.599][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.599][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:07.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:07.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.600][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.601][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.601][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:07.601][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:07.601][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.602][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.602][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-25 18:58:07.602][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.603][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-25 18:58:07.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.603][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:07.603][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.604][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.604][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.604][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.604][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-25 18:58:07.605][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:07.605][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.605][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-25 18:58:07.605][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:07.606][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.606][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.606][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.606][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-25 18:58:07.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.607][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:07.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.608][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.608][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.608][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:07.609][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:07.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.609][self$setPropertyValue]
biodb.DEBUG[2025-02-25 18:58:07.609][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:58:07.610][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.622][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[2025-02-25 18:58:07.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.626][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[2025-02-25 18:58:07.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.630][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-25 18:58:07.630][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-25 18:58:07.631][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-25 18:58:07.631][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-25 18:58:07.631][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:58:07.632][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-25 18:58:07.632][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-25 18:58:07.632][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-25 18:58:07.633][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-25 18:58:07.633][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-25 18:58:07.633][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:58:07.634][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-25 18:58:07.634][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-25 18:58:07.635][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-25 18:58:07.635][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-25 18:58:07.635][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-25 18:58:07.636][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-25 18:58:07.636][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-25 18:58:07.636][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:58:07.637][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-25 18:58:07.637][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-25 18:58:07.637][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-25 18:58:07.638][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-25 18:58:07.638][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-25 18:58:07.639][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-25 18:58:07.639][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-25 18:58:07.639][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-25 18:58:07.640][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-25 18:58:07.640][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-25 18:58:07.640][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-25 18:58:07.641][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-25 18:58:07.641][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-25 18:58:07.641][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-25 18:58:07.642][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-25 18:58:07.642][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-25 18:58:07.642][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-25 18:58:07.643][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-25 18:58:07.643][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-25 18:58:07.644][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-25 18:58:07.644][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-25 18:58:07.644][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-25 18:58:07.645][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-25 18:58:07.645][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-25 18:58:07.645][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-25 18:58:07.646][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-25 18:58:07.646][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-25 18:58:07.646][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-25 18:58:07.647][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-25 18:58:07.647][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-25 18:58:07.647][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-25 18:58:07.648][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-25 18:58:07.648][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-25 18:58:07.649][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-25 18:58:07.649][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-25 18:58:07.649][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-25 18:58:07.650][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-25 18:58:07.650][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-25 18:58:07.650][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-25 18:58:07.651][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-25 18:58:07.651][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-25 18:58:07.652][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-25 18:58:07.652][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-25 18:58:07.652][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-25 18:58:07.653][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-25 18:58:07.653][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-25 18:58:07.653][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-25 18:58:07.654][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:58:07.654][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:58:07.654][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-25 18:58:07.655][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-25 18:58:07.655][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-25 18:58:07.655][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-25 18:58:07.656][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-25 18:58:07.656][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-25 18:58:07.657][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-25 18:58:07.657][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-25 18:58:07.657][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-25 18:58:07.658][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-25 18:58:07.658][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-25 18:58:07.658][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-25 18:58:07.659][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-25 18:58:07.659][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-25 18:58:07.659][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-25 18:58:07.660][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-25 18:58:07.660][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-25 18:58:07.661][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-25 18:58:07.661][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.661][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.665][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.DEBUG[2025-02-25 18:58:07.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.668][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[2025-02-25 18:58:07.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.671][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[2025-02-25 18:58:07.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.678][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[2025-02-25 18:58:07.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.680][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[2025-02-25 18:58:07.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-25 18:58:07.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.691][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[2025-02-25 18:58:07.692][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-02-25 18:58:07.692][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-02-25 18:58:07.693][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.693][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-25 18:58:07.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.694][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.694][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.694][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-02-25 18:58:07.695][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-25 18:58:07.695][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-25 18:58:07.695][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-02-25 18:58:07.696][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-25 18:58:07.697][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-25 18:58:07.697][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-25 18:58:07.697][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-25 18:58:07.697][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-25 18:58:07.697][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.698][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-25 18:58:07.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-25 18:58:07.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-25 18:58:07.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-25 18:58:07.699][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:58:07.699][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-02-25 18:58:07.699][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-25 18:58:07.699][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-25 18:58:07.699][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-25 18:58:07.700][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-02-25 18:58:07.700][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-02-25 18:58:07.700][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-25 18:58:07.700][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-25 18:58:07.701][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-02-25 18:58:07.701][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-25 18:58:07.702][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-25 18:58:07.702][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-25 18:58:07.703][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-02-25 18:58:07.704][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-02-25 18:58:07.704][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-02-25 18:58:07.704][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-02-25 18:58:07.705][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:58:07.705][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-25 18:58:07.705][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-02-25 18:58:07.705][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-02-25 18:58:07.706][biodb::testThat]
biodb.INFO [2025-02-25 18:58:07.706][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-02-25 18:58:07.706][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-25 18:58:07.707][biodb::testThat]
biodb.DEBUG[2025-02-25 18:58:07.708][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-02-25 18:58:07.709][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:58:07.709][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-02-25 18:58:07.710][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:58:07.710][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-02-25 18:58:07.711][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-02-25 18:58:07.712][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-02-25 18:58:07.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-02-25 18:58:07.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-02-25 18:58:07.713][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-02-25 18:58:07.715][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-02-25 18:58:07.715][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-02-25 18:58:07.716][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-02-25 18:58:07.716][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-02-25 18:58:07.716][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-02-25 18:58:07.717][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-02-25 18:58:07.717][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-02-25 18:58:07.717][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-02-25 18:58:07.718][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-02-25 18:58:07.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:07.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:07.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:07.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:07.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:07.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:07.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-25 18:58:07.722][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-02-25 18:58:07.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-02-25 18:58:07.723][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-02-25 18:58:07.723][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-02-25 18:58:08.957][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-02-25 18:58:10.109][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-02-25 18:58:10.110][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-02-25 18:58:10.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-02-25 18:58:10.112][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-02-25 18:58:10.113][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-02-25 18:58:10.113][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-02-25 18:58:10.113][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-02-25 18:58:10.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-25 18:58:10.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:10.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:10.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:10.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:10.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:10.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-25 18:58:10.118][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.119][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.119][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.121][ef$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:58:10.121][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:58:10.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.122][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.122][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-02-25 18:58:10.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-02-25 18:58:10.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.123][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:58:10.123][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:58:10.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.124][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-25 18:58:10.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-25 18:58:10.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.125][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-25 18:58:10.126][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-25 18:58:10.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.126][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.126][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-25 18:58:10.127][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-25 18:58:10.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.127][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.128][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:58:10.128][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:58:10.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.128][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.129][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:58:10.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-25 18:58:10.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.130][ef$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:58:10.130][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:58:10.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.131][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.131][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-02-25 18:58:10.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-25 18:58:10.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.132][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:58:10.132][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:58:10.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.133][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:58:10.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-25 18:58:10.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.134][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:58:10.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:58:10.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.135][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-25 18:58:10.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-25 18:58:10.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:58:10.137][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:58:10.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.137][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.138][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-02-25 18:58:10.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-02-25 18:58:10.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.139][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:58:10.139][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:58:10.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.139][ef$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.140][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-25 18:58:10.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-25 18:58:10.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:58:10.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:58:10.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:58:10.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:58:10.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-25 18:58:10.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-25 18:58:10.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-25 18:58:10.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-25 18:58:10.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-25 18:58:10.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-25 18:58:10.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-25 18:58:10.152][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-02-25 18:58:10.153][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-25 18:58:10.153][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-02-25 18:58:10.154][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-02-25 18:58:10.154][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-25 18:58:10.154][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-25 18:58:10.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-25 18:58:10.155][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-25 18:58:10.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-25 18:58:10.155][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-25 18:58:10.155][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
  5.506   0.430 114.457

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	0.762	0.235	2.826
ChebiEntry	0.108	0.006	0.114