Multiple platform build/check report for BioC 3.21 - CHECK results for biodbChebi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4823
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4565
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4603
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4544
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for biodbChebi on merida1

To the developers/maintainers of the biodbChebi package:
- 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: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2025-08-01 00:29:54 -0400 (Fri, 01 Aug 2025)

EndedAt: 2025-08-01 00:32:44 -0400 (Fri, 01 Aug 2025)

EllapsedTime: 169.6 seconds

RetCode: 0

Status: OK

CheckDir: biodbChebi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 4.412  1.239   6.645
* 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-x86_64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.14.0’
** 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 version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-08-01 00:31:22.089][biodb::testContext]
biodb.INFO [2025-08-01 00:31:22.095][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:31:22.098][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-08-01 00:31:22.100][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:31:22.102][biodb::testContext]
biodb.INFO [2025-08-01 00:31:22.113][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:31:22.117][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-01 00:31:22.130][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:31:22.133][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-01 00:31:22.135][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-01 00:31:22.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.145][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-01 00:31:22.194][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-01 00:31:22.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.203][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-01 00:31:22.206][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-01 00:31:22.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.215][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-01 00:31:22.218][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-01 00:31:22.220][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-01 00:31:22.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.226][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[2025-08-01 00:31:22.229][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-01 00:31:22.231][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-01 00:31:22.234][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-01 00:31:22.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.243][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-01 00:31:22.246][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-01 00:31:22.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.256][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-01 00:31:22.258][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-01 00:31:22.261][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-01 00:31:22.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.270][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-01 00:31:22.272][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-01 00:31:22.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.281][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-01 00:31:22.283][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-01 00:31:22.286][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-01 00:31:22.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.294][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:31:22.296][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-01 00:31:22.298][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-01 00:31:22.301][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-01 00:31:22.303][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-01 00:31:22.306][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-01 00:31:22.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.314][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-01 00:31:22.317][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-01 00:31:22.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.325][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-01 00:31:22.327][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-01 00:31:22.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.333][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[2025-08-01 00:31:22.335][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-01 00:31:22.336][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-01 00:31:22.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.344][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-01 00:31:22.346][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-01 00:31:22.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.355][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-01 00:31:22.357][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-01 00:31:22.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.366][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:31:22.368][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-01 00:31:22.387][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-01 00:31:22.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.397][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-01 00:31:22.399][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-01 00:31:22.402][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-01 00:31:22.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.417][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-01 00:31:22.503][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.553][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-01 00:31:22.555][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:31:22.560][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.562][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.570][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:31:22.572][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:31:22.575][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.577][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-01 00:31:22.580][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:31:22.582][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.584][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.587][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:31:22.587][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:31:22.587][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:31:22.587][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:31:22.587][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:31:22.589][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:31:22.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.596][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:31:22.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.605][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.607][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:31:22.609][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:31:22.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.615][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.618][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-01 00:31:22.622][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.625][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:31:22.627][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:31:22.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.635][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.637][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.640][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.642][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:31:22.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:31:22.647][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.649][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-01 00:31:22.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:31:22.654][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.656][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:31:22.657][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:31:22.657][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:31:22.657][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:31:22.657][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:31:22.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:31:22.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.663][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:31:22.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.668][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.670][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.673][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.675][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:31:22.677][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:31:22.680][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.685][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-01 00:31:22.689][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.692][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-01 00:31:22.694][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.697][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:31:22.699][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.704][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.707][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.709][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:31:22.712][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:31:22.714][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.717][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-01 00:31:22.719][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:31:22.721][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.724][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.726][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.729][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:31:22.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.735][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:31:22.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.740][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.744][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.746][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:31:22.747][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:31:22.749][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.750][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.752][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-01 00:31:22.756][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.758][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:31:22.760][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.762][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:31:22.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.765][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.766][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.769][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:31:22.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:31:22.772][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.773][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-01 00:31:22.775][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:31:22.778][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:22.783][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.785][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:31:22.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.791][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:31:22.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:22.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:22.798][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:31:22.800][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.802][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:31:22.805][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:31:22.807][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:22.810][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:31:22.818][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:31:22.820][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.844][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.DEBUG[2025-08-01 00:31:22.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.853][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.DEBUG[2025-08-01 00:31:22.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.864][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.DEBUG[2025-08-01 00:31:22.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:22.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:22.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:22.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:22.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:22.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.012][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[2025-08-01 00:31:23.014][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-01 00:31:23.024][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-01 00:31:23.028][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-01 00:31:23.031][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-01 00:31:23.035][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:31:23.039][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-01 00:31:23.042][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-01 00:31:23.045][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-01 00:31:23.049][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-01 00:31:23.052][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-01 00:31:23.055][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:31:23.059][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-01 00:31:23.062][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-01 00:31:23.066][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-01 00:31:23.070][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-01 00:31:23.073][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-01 00:31:23.077][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-01 00:31:23.081][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-01 00:31:23.084][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:31:23.088][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-01 00:31:23.091][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-01 00:31:23.095][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-01 00:31:23.098][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-01 00:31:23.102][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-01 00:31:23.105][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-01 00:31:23.109][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-01 00:31:23.112][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-01 00:31:23.115][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-01 00:31:23.119][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-01 00:31:23.122][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-01 00:31:23.126][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-01 00:31:23.129][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-01 00:31:23.132][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-01 00:31:23.135][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-01 00:31:23.138][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-01 00:31:23.142][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-01 00:31:23.145][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-01 00:31:23.148][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-01 00:31:23.152][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-01 00:31:23.155][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-01 00:31:23.158][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-01 00:31:23.162][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-01 00:31:23.165][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-01 00:31:23.169][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-01 00:31:23.173][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-01 00:31:23.176][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-01 00:31:23.180][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-01 00:31:23.183][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-01 00:31:23.187][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-01 00:31:23.190][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-01 00:31:23.194][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-01 00:31:23.197][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-01 00:31:23.200][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-01 00:31:23.203][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-01 00:31:23.207][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-01 00:31:23.210][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-01 00:31:23.214][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-01 00:31:23.217][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-01 00:31:23.220][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-01 00:31:23.223][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-01 00:31:23.227][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-01 00:31:23.230][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-01 00:31:23.234][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-01 00:31:23.238][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-01 00:31:23.241][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-01 00:31:23.244][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-01 00:31:23.248][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:31:23.251][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:31:23.254][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-01 00:31:23.258][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-01 00:31:23.261][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-01 00:31:23.265][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-01 00:31:23.268][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-01 00:31:23.272][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-01 00:31:23.275][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-01 00:31:23.278][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-01 00:31:23.282][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-01 00:31:23.285][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-01 00:31:23.289][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-01 00:31:23.292][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-01 00:31:23.296][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-01 00:31:23.299][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-01 00:31:23.302][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-01 00:31:23.316][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-01 00:31:23.320][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:31:23.327][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:31:23.329][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.333][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.455][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[2025-08-01 00:31:23.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.472][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[2025-08-01 00:31:23.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.515][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[2025-08-01 00:31:23.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.544][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[2025-08-01 00:31:23.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:23.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.604][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[2025-08-01 00:31:23.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.620][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[2025-08-01 00:31:23.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:31:23.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.635][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.DEBUG[2025-08-01 00:31:23.639][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-01 00:31:23.664][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-01 00:31:23.669][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:23.672][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-01 00:31:23.674][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:23.677][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:31:23.680][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:23.682][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:31:23.685][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:23.687][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-01 00:31:23.689][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-01 00:31:23.692][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:31:23.695][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:23.697][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-01 00:31:23.700][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-01 00:31:23.703][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-01 00:31:23.706][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-01 00:31:23.709][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:31:23.709][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:31:23.709][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:31:23.712][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-01 00:31:23.714][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:23.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:23.719][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:31:23.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:31:23.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:31:23.725][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:31:23.728][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:23.728][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-01 00:31:23.730][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:31:23.732][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:31:23.734][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-01 00:31:23.736][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-01 00:31:23.736][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-01 00:31:23.751][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:31:23.755][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:31:23.759][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-01 00:31:23.763][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:31:23.767][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:31:23.771][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:31:23.858][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-01 00:31:23.861][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-01 00:31:23.867][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-01 00:31:23.874][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-01 00:31:23.882][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:31:23.884][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:31:23.887][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-01 00:31:23.890][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-01 00:31:23.907][biodb::testThat]
biodb.INFO [2025-08-01 00:31:23.910][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-01 00:31:23.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:23.914][biodb::testThat]
biodb.TRACE[2025-08-01 00:31:23.922][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-08-01 00:31:23.926][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:23.932][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:23.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:23.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:23.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:23.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:23.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:23.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:23.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:24.000][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.002][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.006][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.051][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:24.054][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:24.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.059][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.127][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:24.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:24.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.136][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:24.139][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:24.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.144][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:24.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:24.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.156][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:24.159][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:24.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.164][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:24.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:24.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.177][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.181][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.185][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.197][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:24.200][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:24.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.204][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.207][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:24.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:24.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.217][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:24.220][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:24.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.224][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.227][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:24.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:24.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.238][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:24.240][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:24.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.245][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:24.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.271][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:24.273][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:24.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.278][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:24.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.290][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:24.292][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:24.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.296][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.299][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:24.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:24.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.308][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:24.310][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:24.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.313][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:24.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:24.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:24.503][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-08-01 00:31:24.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:24.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:24.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:24.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:24.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:24.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:24.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:24.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:24.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:24.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.630][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-01 00:31:24.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-01 00:31:24.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.640][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-01 00:31:24.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-01 00:31:24.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-01 00:31:24.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-01 00:31:24.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.659][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-01 00:31:24.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-01 00:31:24.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.964][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.971][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:24.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:24.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:24.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:24.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.038][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.045][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:25.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:25.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:25.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:25.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:25.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:25.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:25.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.103][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:25.106][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:25.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.110][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:25.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:25.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:25.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:25.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.150][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:25.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:25.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:25.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.170][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:25.173][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:25.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.178][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:25.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:25.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.238][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.246][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.304][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.307][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.311][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.342][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:25.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:25.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.359][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:25.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.401][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:25.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:25.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.411][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:25.414][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:25.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.418][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.420][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:25.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.467][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.477][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.488][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.499][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.502][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.507][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.509][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.558][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.568][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.570][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.575][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.577][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.607][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:25.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:25.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.617][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:25.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:25.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:25.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:25.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.636][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:25.638][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:25.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.643][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:25.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:25.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.707][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.710][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.715][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:25.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:25.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:25.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:25.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:25.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:25.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.781][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:25.784][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:25.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.788][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:25.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:25.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.818][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:25.821][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:25.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.826][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.836][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:25.839][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:25.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.844][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.855][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:25.858][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:25.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.863][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.876][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:25.879][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:25.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.883][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.898][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:25.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.902][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.914][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.916][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:25.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.920][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.932][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:25.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.940][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.952][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:25.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.958][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.969][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.972][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:25.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.977][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:25.989][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:25.992][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:25.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:25.997][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.009][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:26.012][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:26.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.017][ef$get] fields variable is a list.
biodb.INFO [2025-08-01 00:31:26.036][biodb::testThat]
biodb.INFO [2025-08-01 00:31:26.038][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-01 00:31:26.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:26.042][biodb::testThat]
biodb.DEBUG[2025-08-01 00:31:26.076][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-08-01 00:31:26.090][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:26.099][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-08-01 00:31:26.102][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:31:26.105][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-08-01 00:31:26.108][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:26.181][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:26.184][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:26.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:26.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:26.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:26.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:26.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:26.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:26.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:26.214][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.217][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.220][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.282][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:26.284][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:26.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.289][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.291][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:26.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:26.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.302][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:26.304][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:26.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.309][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:26.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:26.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.322][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:26.324][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:26.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.329][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:26.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:26.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.342][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:26.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:26.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.349][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:26.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:26.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.362][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:26.364][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:26.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.369][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.372][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:26.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:26.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.384][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:26.386][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:26.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.391][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.394][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:26.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:26.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.404][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:26.407][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:26.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.411][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:26.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:26.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.423][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:26.425][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:26.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.429][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:26.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:26.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.444][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:26.447][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:26.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.451][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.454][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:26.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:26.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.463][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:26.474][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:26.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.478][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.481][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:26.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:26.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:26.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:26.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:26.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:26.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:26.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:26.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:26.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:26.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:26.580][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-08-01 00:31:26.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-01 00:31:26.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-01 00:31:26.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-01 00:31:26.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-01 00:31:26.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-01 00:31:26.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-01 00:31:26.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-01 00:31:26.627][biodb::testThat]
biodb.INFO [2025-08-01 00:31:26.630][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-01 00:31:26.632][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:26.634][biodb::testThat]
biodb.TRACE[2025-08-01 00:31:26.641][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:26.644][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:26.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.649][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:26.651][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-08-01 00:31:26.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:26.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:26.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:26.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:26.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:26.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:26.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:26.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:26.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:26.756][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-08-01 00:31:26.762][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-01 00:31:26.825][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:31:26.866][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-01 00:31:26.870][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:31:26.873][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-01 00:31:26.934][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[2025-08-01 00:31:26.941][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:26.944][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:26.947][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:31:27.629][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:31:28.126][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:28.130][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-08-01 00:31:28.167][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-08-01 00:31:28.172][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-08-01 00:31:28.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:28.204][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:28.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.208][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.211][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.213][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.218][ef$get] fields variable is a list.
biodb.INFO [2025-08-01 00:31:28.228][biodb::testThat]
biodb.INFO [2025-08-01 00:31:28.231][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-01 00:31:28.233][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:28.235][biodb::testThat]
biodb.TRACE[2025-08-01 00:31:28.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:28.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:28.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:28.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:28.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:28.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:28.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:28.487][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:31:28.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:31:28.498][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-01 00:31:28.501][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:31:28.504][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-08-01 00:31:28.552][biodb::testThat]
biodb.INFO [2025-08-01 00:31:28.554][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-01 00:31:28.556][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:28.558][biodb::testThat]
biodb.TRACE[2025-08-01 00:31:28.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:28.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:28.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:28.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:28.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-01 00:31:28.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-01 00:31:28.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.697][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-01 00:31:28.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-01 00:31:28.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:28.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:28.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:28.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:28.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.748][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:28.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:28.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.803][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-01 00:31:28.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.812][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-01 00:31:28.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-01 00:31:28.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:28.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-01 00:31:28.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-01 00:31:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-01 00:31:28.840][biodb::testThat]
biodb.INFO [2025-08-01 00:31:28.842][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-01 00:31:28.844][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:28.846][biodb::testThat]
biodb.INFO [2025-08-01 00:31:28.863][biodb::testThat]
biodb.INFO [2025-08-01 00:31:28.865][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-01 00:31:28.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:28.870][biodb::testThat]
biodb.INFO [2025-08-01 00:31:28.887][biodb::testThat]
biodb.INFO [2025-08-01 00:31:28.889][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-01 00:31:28.891][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:28.894][biodb::testThat]
biodb.DEBUG[2025-08-01 00:31:28.902][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-08-01 00:31:29.443][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-08-01 00:31:30.172][biodb::testThat]
biodb.INFO [2025-08-01 00:31:30.175][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-01 00:31:30.178][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:30.180][biodb::testThat]
biodb.DEBUG[2025-08-01 00:31:30.581][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-08-01 00:31:30.984][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:30.987][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:30.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:30.991][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:30.994][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:30.996][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:30.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.001][ef$get] fields variable is a list.
biodb.INFO [2025-08-01 00:31:31.005][biodb::testThat]
biodb.INFO [2025-08-01 00:31:31.007][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-08-01 00:31:31.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:31:31.012][biodb::testThat]
biodb.TRACE[2025-08-01 00:31:31.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:31.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:31.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:31.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:31.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:31.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:31.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:31.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:31.244][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:31:31.251][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:31:31.255][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-01 00:31:31.258][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:31:31.261][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-01 00:31:31.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:31:31.425][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:31:31.429][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-01 00:31:31.432][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:31:31.435][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-08-01 00:31:31.467][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-01 00:31:31.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-01 00:31:31.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:31.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:31.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:31.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:31.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:31.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:31.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:31.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:31.555][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:31:31.597][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:31.599][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:31.639][private$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[2025-08-01 00:31:32.026][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[2025-08-01 00:31:32.409][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:32.414][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-08-01 00:31:32.443][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-08-01 00:31:32.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:32.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:32.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:32.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:32.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:32.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:32.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:32.476][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-08-01 00:31:32.621][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:32.625][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-08-01 00:31:32.652][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:32.654][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:32.657][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:32.659][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:32.661][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:32.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:32.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:32.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:32.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:32.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:32.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:32.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:32.693][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.DEBUG[2025-08-01 00:31:32.696][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-08-01 00:31:32.703][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:32.706][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:32.710][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-08-01 00:31:33.094][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-08-01 00:31:33.479][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:33.484][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-08-01 00:31:33.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-08-01 00:31:33.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-08-01 00:31:33.503][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:33.506][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:33.509][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:33.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:33.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:33.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:33.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:33.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:33.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:33.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:33.540][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.542][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.560][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.573][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:33.576][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:33.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.581][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.584][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:33.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:33.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.595][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:33.598][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:33.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.602][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.606][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:33.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:33.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.616][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:33.619][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:33.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.623][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:33.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:33.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.636][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:33.639][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:33.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.644][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:33.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:33.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.656][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:33.658][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:33.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.663][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.666][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:33.668][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.672][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.675][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:33.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.685][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:33.687][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:33.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.692][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:33.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:33.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.704][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:33.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:33.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.711][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:33.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:33.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.725][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:33.727][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:33.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.732][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.735][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:33.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:33.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.746][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:33.749][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:33.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.777][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:33.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:33.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:33.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:33.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:33.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:33.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:33.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:33.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:33.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:33.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:33.933][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-08-01 00:31:33.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:33.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:33.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:33.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:33.986][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[2025-08-01 00:31:33.995][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:33.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:34.002][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:31:34.389][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:31:34.771][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:34.776][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-08-01 00:31:34.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-08-01 00:31:34.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:34.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:34.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:34.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:34.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:34.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:34.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:34.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:34.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:34.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:34.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:34.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:34.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:34.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:34.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:34.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:34.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:34.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:34.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:34.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:34.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:34.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:34.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:34.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:34.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:34.918][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-08-01 00:31:34.921][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:34.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-08-01 00:31:34.927][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:34.929][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:34.932][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:34.935][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:34.936][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:34.938][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:34.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:34.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:34.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:34.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:34.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:34.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:34.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:34.997][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-08-01 00:31:35.004][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:35.006][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:35.010][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-08-01 00:31:35.393][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-08-01 00:31:35.775][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:35.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-08-01 00:31:35.790][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-08-01 00:31:35.796][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-08-01 00:31:35.799][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:35.802][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:35.805][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:35.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:35.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:35.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:35.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:35.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:35.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:35.844][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[2025-08-01 00:31:35.848][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:35.851][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:35.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.855][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:35.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:35.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.866][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:35.868][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:35.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.872][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.875][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:35.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:35.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.884][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:35.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:35.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.891][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:35.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:35.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.905][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:35.907][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:35.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.912][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:35.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:35.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.924][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:35.926][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:35.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.931][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:35.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.943][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:35.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:35.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.950][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.953][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:35.956][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:35.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.960][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.962][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:35.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:35.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.972][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:35.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:35.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.980][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:35.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:35.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:35.992][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:35.995][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:35.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:35.999][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:36.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:36.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.012][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:36.015][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:36.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.022][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:36.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:36.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.032][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:36.035][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:36.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.039][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.042][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:36.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:36.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:36.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:36.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:36.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:36.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:36.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:36.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:36.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:36.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:36.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:36.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:36.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:36.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:36.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:36.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:36.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:36.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:36.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:36.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:36.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:36.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:36.217][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-08-01 00:31:36.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:36.354][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:31:36.363][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:31:36.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-01 00:31:36.369][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:31:36.372][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-01 00:31:36.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:36.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:36.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:36.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:36.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:36.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:36.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:36.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:36.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:36.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:36.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:36.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:36.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:36.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:36.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:36.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:36.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:36.462][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-08-01 00:31:36.464][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:36.468][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-08-01 00:31:36.471][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:36.473][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:36.476][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:36.479][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:36.481][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:36.483][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:36.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:36.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:36.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:36.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:36.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:36.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:36.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:36.513][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-08-01 00:31:36.519][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:36.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:36.524][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-08-01 00:31:36.904][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-08-01 00:31:37.289][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:37.294][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-08-01 00:31:37.330][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-08-01 00:31:37.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-08-01 00:31:37.341][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:37.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:37.348][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:37.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:37.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:37.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:37.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:37.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:37.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:37.376][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.TRACE[2025-08-01 00:31:37.382][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.385][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.390][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.405][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:37.408][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:37.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.413][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.417][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:37.420][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:37.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.425][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.429][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:37.431][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:37.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.436][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.439][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:37.443][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:37.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.451][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:37.454][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:37.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.458][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.461][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:37.464][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.482][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.486][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:37.488][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:37.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.494][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.496][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:37.500][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:37.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.504][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:37.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:37.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.519][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:37.522][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:37.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.527][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.530][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:37.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:37.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.542][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:37.545][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:37.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.551][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:37.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:37.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:37.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:37.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:37.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:37.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:37.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:37.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:37.659][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-08-01 00:31:37.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:37.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:37.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:37.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:37.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:37.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:37.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:37.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:37.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:37.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:37.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:37.750][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-08-01 00:31:37.752][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:37.757][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-08-01 00:31:37.760][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:37.762][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:37.765][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:37.768][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:37.770][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:37.773][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:37.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:37.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:37.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:37.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:37.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:37.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:37.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:37.808][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-08-01 00:31:37.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:37.817][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:37.820][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-08-01 00:31:38.203][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-08-01 00:31:38.589][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:38.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-08-01 00:31:38.599][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-08-01 00:31:38.608][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-08-01 00:31:38.612][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:38.615][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:38.618][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:38.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:38.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:38.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:38.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:38.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:38.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:38.644][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.TRACE[2025-08-01 00:31:38.649][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.652][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.656][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.670][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:38.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:38.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.677][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.680][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:38.683][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:38.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.688][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.691][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:38.694][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:38.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.698][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.701][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:38.703][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:38.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.707][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.709][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:38.712][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:38.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.716][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.719][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:38.721][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.724][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.726][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:38.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:38.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.734][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.736][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:38.739][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:38.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.758][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:38.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:38.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.774][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:38.777][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:38.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.781][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.784][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:38.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:38.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.795][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:38.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:38.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.803][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:38.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:38.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:38.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:38.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:38.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:38.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:38.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:38.899][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-08-01 00:31:38.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:38.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:38.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:38.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:38.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:38.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:38.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:38.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:38.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:38.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:38.974][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-08-01 00:31:38.977][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:38.981][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-08-01 00:31:38.984][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:38.987][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:38.997][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:39.000][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:39.003][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:39.005][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:39.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:39.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:39.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:39.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:39.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:39.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:39.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:39.032][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-08-01 00:31:39.039][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:39.041][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:39.044][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-08-01 00:31:39.429][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-08-01 00:31:39.812][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:39.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-08-01 00:31:39.854][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-08-01 00:31:39.860][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-08-01 00:31:39.864][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:39.866][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:39.869][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:39.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:39.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:39.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:39.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:39.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:39.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:39.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:39.900][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:39.903][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:39.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.907][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:39.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:39.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.919][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:39.922][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:39.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.926][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.928][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:39.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:39.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.934][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.937][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:39.940][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:39.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.944][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:39.949][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:39.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.953][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.956][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:39.958][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:39.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.962][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.965][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:39.968][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:39.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.972][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:39.976][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:39.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.978][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.980][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:39.981][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:39.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.984][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:39.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:39.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:39.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:39.992][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:39.994][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:40.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.009][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.012][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:40.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:40.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:40.023][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:40.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.025][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:40.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:40.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:40.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:40.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:40.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:40.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:40.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:40.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:40.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:40.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:40.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:40.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:40.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:40.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:40.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:40.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:40.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:40.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:40.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:40.099][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-08-01 00:31:40.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:40.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:40.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:40.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:40.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:40.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:40.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:40.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:40.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:40.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:40.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:40.169][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-08-01 00:31:40.172][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:40.177][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-08-01 00:31:40.180][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:40.182][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:40.184][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:40.186][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:40.188][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:40.189][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:40.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:40.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:40.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:40.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:40.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:40.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:40.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:40.222][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-08-01 00:31:40.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:40.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:40.235][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-08-01 00:31:40.620][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-08-01 00:31:41.014][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:41.018][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-08-01 00:31:41.026][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-08-01 00:31:41.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-08-01 00:31:41.036][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:41.039][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:41.042][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:41.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:41.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:41.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:41.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:41.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:41.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:41.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:41.070][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.071][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.074][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.086][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:41.089][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:41.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.094][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.097][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:41.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:41.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.106][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:41.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:41.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:41.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:41.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.127][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:41.129][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:41.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.133][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:41.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:41.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.146][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:41.148][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:41.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.152][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:41.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:41.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.164][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:41.166][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:41.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.170][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.173][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:41.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:41.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.182][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:41.185][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.189][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.192][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:41.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.214][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:41.217][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:41.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:41.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:41.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.229][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:41.231][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:41.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.233][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:41.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.247][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:41.249][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:41.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.253][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:41.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.266][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:41.268][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:41.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.273][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.276][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:41.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:41.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:41.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:41.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:41.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:41.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:41.376][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-08-01 00:31:41.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:41.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:41.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:41.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:41.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:41.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:41.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:41.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:41.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:41.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:41.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:41.436][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-08-01 00:31:41.438][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:41.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-08-01 00:31:41.445][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:41.447][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:41.450][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:41.452][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:41.454][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:41.456][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:41.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:41.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:41.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:41.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:41.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:41.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:41.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:41.485][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-08-01 00:31:41.491][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:41.494][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:41.497][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-08-01 00:31:41.882][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-08-01 00:31:42.276][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:42.281][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-08-01 00:31:42.289][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-08-01 00:31:42.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-08-01 00:31:42.301][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:42.304][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:42.308][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:42.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:42.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:42.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:42.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:42.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:42.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:42.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:42.339][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.342][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.347][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.359][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:42.361][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:42.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.368][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:42.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.378][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:42.380][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:42.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.385][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:42.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.399][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:42.402][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:42.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.407][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:42.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.421][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:42.424][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:42.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.443][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:42.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:42.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.458][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:42.461][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:42.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.467][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.470][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:42.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:42.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.485][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:42.487][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.492][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.495][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:42.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:42.507][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:42.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:42.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:42.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.524][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:42.526][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:42.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.530][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:42.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:42.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.543][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:42.546][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:42.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.551][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.554][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:42.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:42.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.565][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:42.567][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:42.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.572][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:42.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:42.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:42.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:42.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:42.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:42.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:42.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:42.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:42.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:42.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:42.689][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-08-01 00:31:42.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:42.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:42.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:42.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:42.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:42.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:42.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:42.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:42.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:42.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:42.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:42.748][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-08-01 00:31:42.750][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:42.754][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-08-01 00:31:42.757][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:42.760][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:42.762][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:42.765][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:42.767][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:42.770][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:42.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:42.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:42.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:42.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:42.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:42.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:42.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:42.803][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-08-01 00:31:42.810][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:42.813][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:42.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-08-01 00:31:43.200][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-08-01 00:31:43.591][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:43.596][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-08-01 00:31:43.604][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-08-01 00:31:43.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-08-01 00:31:43.650][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:43.653][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:43.656][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:43.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:43.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:43.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:43.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:43.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:43.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:43.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:43.689][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.696][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.709][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:43.712][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:43.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.716][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.719][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:43.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:43.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.729][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:43.745][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:43.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.749][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.752][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:43.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:43.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.762][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:43.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:43.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.769][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:43.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:43.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:43.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:43.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.785][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:43.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:43.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.796][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:43.798][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:43.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.802][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.804][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:43.807][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:43.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.811][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.814][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:43.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:43.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:43.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:43.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.830][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:43.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:43.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.843][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:43.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:43.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.850][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:43.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:43.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.862][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:43.865][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:43.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.869][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.872][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:43.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:43.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.882][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:43.885][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:43.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.890][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:43.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:43.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:43.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:43.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:43.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:43.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:43.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:43.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:43.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:44.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:44.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:44.007][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-08-01 00:31:44.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:44.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:44.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:44.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:44.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:44.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:44.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:44.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:44.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:44.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:44.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:44.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:44.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:44.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:44.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:44.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:44.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:44.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:44.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:44.075][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-08-01 00:31:44.077][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:44.081][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-08-01 00:31:44.084][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:44.087][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:44.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:44.092][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:44.095][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:44.097][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:44.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:44.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:44.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:44.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:44.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:44.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:44.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:44.127][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-08-01 00:31:44.134][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:44.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:44.140][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-08-01 00:31:44.523][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-08-01 00:31:44.912][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:44.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-08-01 00:31:44.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-08-01 00:31:44.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-08-01 00:31:44.935][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:44.938][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:44.941][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:44.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:44.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:44.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:44.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:44.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:44.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:44.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:44.973][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:44.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:44.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:44.992][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:44.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:44.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.005][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:45.007][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:45.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.011][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.014][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:45.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:45.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.023][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:45.025][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:45.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.029][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:45.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.041][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:45.044][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:45.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.049][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:45.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:45.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.061][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:45.064][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:45.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.068][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:45.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:45.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.081][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:45.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:45.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.091][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:45.094][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.102][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:45.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.112][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:45.115][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:45.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.119][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:45.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:45.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.131][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:45.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:45.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.137][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:45.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:45.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.144][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:45.146][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:45.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.148][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.150][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:45.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:45.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.155][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:45.157][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:45.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.160][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.163][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:45.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:45.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:45.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:45.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:45.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:45.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:45.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:45.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:45.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:45.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:45.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:45.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:45.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:45.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:45.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:45.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:45.278][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-08-01 00:31:45.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:45.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:45.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:45.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:45.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:45.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:45.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:45.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:45.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:45.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:45.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:45.327][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-08-01 00:31:45.329][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:45.334][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-08-01 00:31:45.337][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:45.340][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:45.343][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:45.345][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:45.348][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:45.351][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:45.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:45.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:45.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:45.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:45.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:45.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:45.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:45.383][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-08-01 00:31:45.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:45.392][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:45.396][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-08-01 00:31:45.780][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-08-01 00:31:46.181][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:46.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-08-01 00:31:46.196][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-08-01 00:31:46.201][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-08-01 00:31:46.245][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:46.261][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:46.264][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:46.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:46.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:46.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:46.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:46.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:46.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:46.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:46.293][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.296][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.300][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.311][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:46.314][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:46.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.318][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.321][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:46.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:46.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.331][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:46.333][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:46.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.338][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:46.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:46.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.351][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:46.354][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:46.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.358][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:46.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:46.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.371][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:46.374][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:46.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.378][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:46.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:46.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.390][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:46.392][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:46.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.397][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.400][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:46.403][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.405][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.407][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:46.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.414][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:46.416][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:46.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.420][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:46.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:46.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.433][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:46.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:46.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.440][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:46.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:46.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.452][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:46.454][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:46.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.459][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.461][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:46.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:46.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.471][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:46.474][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:46.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.487][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:46.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:46.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:46.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:46.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:46.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:46.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:46.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:46.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:46.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:46.589][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-08-01 00:31:46.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:46.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:46.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:46.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:46.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:46.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:46.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:46.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:46.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:46.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:46.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:46.635][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-08-01 00:31:46.638][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:46.640][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-08-01 00:31:46.643][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:46.648][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:46.651][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:46.653][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:46.656][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:46.658][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:46.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:46.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:46.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:46.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:46.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:46.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:46.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:46.688][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-08-01 00:31:46.702][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:46.704][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:46.708][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-08-01 00:31:47.090][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-08-01 00:31:47.475][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:47.479][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-08-01 00:31:47.487][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-08-01 00:31:47.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-08-01 00:31:47.496][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:47.499][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:47.501][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:47.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:47.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:47.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:47.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:47.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:47.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:47.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:47.532][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.534][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.538][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.551][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:47.554][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:47.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.558][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.561][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:47.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:47.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.570][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:47.573][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:47.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.578][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.580][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:47.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:47.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.590][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:47.592][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:47.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.597][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:47.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:47.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.612][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:47.615][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:47.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.619][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:47.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.632][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:47.634][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:47.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.638][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.641][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:47.643][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.647][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.650][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:47.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.660][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:47.662][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:47.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.666][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:47.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:47.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.678][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:47.681][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:47.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.699][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:47.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:47.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.711][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:47.713][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:47.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.717][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.720][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:47.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:47.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:47.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:47.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.737][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.743][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:47.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:47.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:47.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:47.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:47.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:47.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:47.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:47.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:47.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:47.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:47.859][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-08-01 00:31:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:47.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:47.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:47.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:47.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:47.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:47.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:47.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:47.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:47.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:47.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:47.916][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-08-01 00:31:47.918][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:47.922][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-08-01 00:31:47.925][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:47.928][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:47.931][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:47.941][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:47.944][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:47.946][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:47.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:47.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:47.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:47.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:47.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:47.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:47.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:47.976][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-08-01 00:31:47.982][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:47.985][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:47.988][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-08-01 00:31:48.368][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-08-01 00:31:48.759][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:48.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-08-01 00:31:48.771][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-08-01 00:31:48.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-08-01 00:31:48.780][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:48.783][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:48.786][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:48.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:48.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:48.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:48.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:48.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:48.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:48.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:48.814][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:48.817][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:48.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.821][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:48.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:48.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.833][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:48.836][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:48.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.840][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.843][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:48.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:48.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.853][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:48.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:48.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.859][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:48.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:48.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.870][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:48.873][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:48.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.876][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:48.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:48.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.888][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:48.890][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:48.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.894][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:48.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:48.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.906][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:48.908][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:48.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.912][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.915][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:48.934][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:48.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.939][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.942][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:48.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:48.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.952][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:48.955][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:48.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.960][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:48.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:48.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.972][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:48.975][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:48.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.979][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:48.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:48.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:48.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:48.994][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:48.996][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:48.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.001][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.004][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:49.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:49.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.014][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:49.017][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:49.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.022][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:49.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:49.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:49.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:49.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:49.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:49.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:49.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:49.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:49.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:49.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:49.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:49.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:49.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:49.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:49.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:49.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:49.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:49.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:49.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:49.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:49.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:49.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:49.124][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-08-01 00:31:49.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:49.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:49.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:49.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:49.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:49.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:49.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:49.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:49.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:49.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:49.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:49.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:49.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:49.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:49.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:49.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:49.209][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-08-01 00:31:49.211][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:49.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-08-01 00:31:49.217][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:49.219][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:49.222][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:49.224][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:49.226][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:49.228][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:49.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:49.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:49.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:49.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:49.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:49.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:49.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:49.257][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-08-01 00:31:49.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:49.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:49.267][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-08-01 00:31:49.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-08-01 00:31:50.035][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:50.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-08-01 00:31:50.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-08-01 00:31:50.054][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-08-01 00:31:50.057][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:50.059][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:50.061][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:50.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:50.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:50.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:50.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:50.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:50.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:50.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:50.086][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.088][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.092][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.104][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:50.106][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:50.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.111][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.114][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:50.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:50.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.123][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:50.125][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:50.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.129][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.131][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:50.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:50.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.138][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:50.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:50.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.145][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.147][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:50.150][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:50.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.166][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.169][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:50.171][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:50.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.176][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.179][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:50.181][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.185][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.188][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:50.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.197][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:50.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:50.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.202][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:50.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:50.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.214][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:50.216][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:50.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.220][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:50.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:50.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.230][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:50.231][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:50.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.234][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.236][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:50.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:50.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.244][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:50.246][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:50.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.251][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:50.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:50.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:50.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:50.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:50.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:50.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:50.340][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-08-01 00:31:50.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:50.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:50.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:50.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:50.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:50.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:50.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:50.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:50.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:50.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:50.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:50.399][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-08-01 00:31:50.402][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:50.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-08-01 00:31:50.407][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:50.410][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:50.413][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:50.415][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:50.417][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:50.419][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:50.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:50.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:50.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:50.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:50.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:50.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:50.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:50.448][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-08-01 00:31:50.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:50.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:50.460][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-08-01 00:31:50.841][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-08-01 00:31:51.224][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:51.227][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-08-01 00:31:51.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-08-01 00:31:51.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-08-01 00:31:51.244][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:51.247][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:51.249][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:51.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:51.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:51.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:51.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:51.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:51.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:51.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:51.277][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.283][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.316][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:51.318][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:51.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.323][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.325][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:51.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.334][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:51.336][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:51.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.340][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.343][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:51.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:51.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.352][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:51.354][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:51.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.358][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.361][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:51.376][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:51.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.381][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.383][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:51.386][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:51.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.391][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.394][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:51.396][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.402][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.405][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:51.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.414][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:51.417][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:51.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.421][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:51.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:51.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.433][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:51.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:51.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.440][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:51.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:51.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.453][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:51.455][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:51.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.460][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.462][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:51.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:51.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.469][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:51.470][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:51.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.473][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:51.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:51.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:51.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:51.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:51.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:51.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:51.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:51.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:51.568][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-08-01 00:31:51.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:51.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:51.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:51.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:51.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:51.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:51.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:51.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:51.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:51.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:51.632][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-08-01 00:31:51.634][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:51.638][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-08-01 00:31:51.641][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:51.644][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:51.646][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:51.649][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:51.651][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:51.653][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:51.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:51.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:51.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:51.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:51.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:51.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:51.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:51.681][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-08-01 00:31:51.687][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:51.689][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:51.692][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-08-01 00:31:52.072][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-08-01 00:31:52.455][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:52.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-08-01 00:31:52.467][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-08-01 00:31:52.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-08-01 00:31:52.477][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:52.480][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:52.483][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:52.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:52.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:52.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:52.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:52.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:52.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:52.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:52.514][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.517][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.521][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.533][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:52.536][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:52.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.540][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.543][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:52.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.553][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:52.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:52.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.560][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.562][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:52.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:52.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.572][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:52.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:52.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.592][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:52.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:52.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.604][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:52.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:52.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.612][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:52.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:52.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.623][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:52.626][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:52.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.631][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.634][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:52.638][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.643][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.645][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:52.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.656][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:52.658][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:52.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.663][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:52.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:52.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.676][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:52.678][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:52.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.683][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:52.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:52.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.696][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:52.699][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:52.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.703][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.705][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:52.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:52.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.715][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:52.717][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:52.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.722][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.725][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:52.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:52.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:52.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:52.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:52.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:52.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:52.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:52.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:52.868][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-08-01 00:31:52.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:52.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:52.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:52.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:52.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:52.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:52.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:52.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:52.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:52.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:52.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:52.924][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-08-01 00:31:52.927][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:52.931][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-08-01 00:31:52.934][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:52.936][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:52.939][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:52.941][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:52.943][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:52.945][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:52.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:52.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:52.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:52.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:52.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:52.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:52.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:52.975][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-08-01 00:31:52.982][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:52.985][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:52.987][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-08-01 00:31:53.371][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-08-01 00:31:53.761][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:53.765][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-08-01 00:31:53.773][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-08-01 00:31:53.778][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-08-01 00:31:53.782][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:53.784][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:53.787][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:53.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:53.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:53.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:53.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:53.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:53.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:53.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:53.814][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:53.817][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:53.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.821][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:53.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:53.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.834][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:53.836][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:53.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.854][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:53.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:53.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.867][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:53.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:53.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.875][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:53.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:53.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.886][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:53.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:53.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.892][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:53.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:53.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.904][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:53.906][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:53.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.911][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:53.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:53.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.923][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:53.926][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:53.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.930][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.932][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:53.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:53.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.939][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.942][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:53.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:53.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.951][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:53.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:53.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.959][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:53.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:53.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.970][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:53.973][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:53.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.978][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:53.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:53.990][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:53.993][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:53.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:53.997][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.000][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:54.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:54.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.008][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:54.010][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:54.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.015][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.018][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:54.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:54.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:54.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:54.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:54.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:54.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:54.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:54.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:54.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:54.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:54.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:54.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:54.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:54.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:54.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:54.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:54.134][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-08-01 00:31:54.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:54.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:54.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:54.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:54.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:54.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:54.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:54.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:54.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:54.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:54.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:54.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:54.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:54.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:54.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:54.183][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-08-01 00:31:54.185][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:54.188][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-08-01 00:31:54.191][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:54.193][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:54.196][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:54.198][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:54.200][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:54.203][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:54.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:54.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:54.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:54.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:54.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:54.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:54.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:54.232][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-08-01 00:31:54.238][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:54.240][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:54.243][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-08-01 00:31:54.626][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-08-01 00:31:55.016][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:55.020][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-08-01 00:31:55.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-08-01 00:31:55.046][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-08-01 00:31:55.050][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:55.052][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:55.055][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:55.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:55.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:55.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:55.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:55.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:55.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:55.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:55.096][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.098][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.102][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.112][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:55.115][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:55.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.143][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:55.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.154][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:55.157][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:55.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.161][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:55.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:55.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.174][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:55.177][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:55.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.179][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:55.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:55.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.191][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:55.194][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:55.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.198][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:55.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:55.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.211][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:55.214][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:55.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.218][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.221][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:55.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.227][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:55.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.238][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:55.241][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:55.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.245][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:55.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:55.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.256][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:55.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:55.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.263][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:55.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:55.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:55.279][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:55.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.284][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.286][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:55.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:55.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.296][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:55.298][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:55.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.302][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.305][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:55.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:55.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:55.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:55.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:55.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:55.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:55.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:55.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:55.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:55.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:55.415][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-08-01 00:31:55.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:55.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:55.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:55.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:55.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:55.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:55.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:55.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:55.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:55.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:55.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:55.466][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-08-01 00:31:55.468][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:55.472][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-08-01 00:31:55.475][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:55.478][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:55.480][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:55.482][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:55.484][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:55.487][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:55.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:55.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:55.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:55.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:55.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:55.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:55.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:55.517][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-08-01 00:31:55.523][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:55.526][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:55.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-08-01 00:31:55.909][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-08-01 00:31:56.299][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:56.318][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-08-01 00:31:56.364][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-08-01 00:31:56.405][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-08-01 00:31:56.409][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:56.412][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:56.415][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:56.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:56.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:56.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:56.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:56.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:56.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:56.442][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[2025-08-01 00:31:56.447][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.455][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.467][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:56.470][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:56.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.474][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:56.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:56.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.485][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:56.488][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:56.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.492][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.495][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:56.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:56.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.504][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:56.506][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:56.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:56.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:56.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.523][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:56.525][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:56.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.530][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:56.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:56.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.542][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:56.544][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:56.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.548][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.551][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:56.554][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.558][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.560][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:56.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:56.572][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:56.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.576][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:56.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.589][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:56.592][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:56.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.595][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:56.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:56.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.607][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:56.616][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:56.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.622][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.625][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:56.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:56.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.635][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:56.638][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:56.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.641][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.643][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:56.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:56.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:56.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:56.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:56.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:56.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:56.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:56.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:56.738][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-08-01 00:31:56.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:56.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:56.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:56.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:56.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:56.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:56.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:56.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:56.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:56.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:56.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:56.792][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-08-01 00:31:56.794][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:56.798][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-08-01 00:31:56.801][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:56.803][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:56.805][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:56.808][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:56.810][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:56.812][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:56.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:56.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:56.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:56.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:56.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:56.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:56.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:56.851][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-08-01 00:31:56.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:56.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:56.863][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-08-01 00:31:57.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-08-01 00:31:57.633][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:57.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-08-01 00:31:57.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-08-01 00:31:57.716][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-08-01 00:31:57.720][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:57.723][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:57.725][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:57.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:57.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:57.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:57.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:57.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:57.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:57.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:57.758][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:57.760][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:57.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.765][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:57.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:57.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.778][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:57.780][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:57.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.785][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:57.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:57.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.797][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:57.800][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:57.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.804][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:57.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:57.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.817][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:57.819][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:57.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.823][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:57.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:57.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.836][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:57.838][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:57.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.843][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:57.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:57.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.855][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:57.857][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:57.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.861][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.864][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:57.867][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:57.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.871][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.873][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:57.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:57.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.895][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:57.898][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:57.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.903][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:57.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:57.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.916][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:57.919][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:57.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.923][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:57.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:57.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.935][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:57.938][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:57.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.942][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.945][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:57.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:57.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.955][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:57.957][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:57.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.962][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.965][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:57.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:57.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:57.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:57.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:57.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:57.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:57.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:57.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:57.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:57.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:58.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:58.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:58.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:58.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:58.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:58.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:58.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:58.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:58.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:58.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:58.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:58.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:58.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:58.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:58.069][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-08-01 00:31:58.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:58.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:58.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:58.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:58.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:58.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:58.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:58.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:58.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:58.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:58.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:58.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:58.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:58.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:58.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:58.134][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-08-01 00:31:58.136][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:58.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-08-01 00:31:58.143][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:58.146][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:58.148][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:58.151][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:58.153][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:58.155][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:58.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:58.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:58.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:58.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:58.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:58.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:58.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:58.185][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-08-01 00:31:58.192][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:58.194][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:58.197][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-08-01 00:31:58.582][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-08-01 00:31:58.968][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:31:58.973][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-08-01 00:31:58.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-08-01 00:31:58.986][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-08-01 00:31:58.989][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:31:58.992][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:31:58.995][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:31:58.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:58.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:59.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:59.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:59.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:59.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:59.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:31:59.022][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.025][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.029][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.042][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:59.044][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:59.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.049][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:31:59.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:31:59.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.061][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:59.064][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:59.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.068][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:31:59.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:31:59.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.080][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:59.083][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:59.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:31:59.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:31:59.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.122][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:59.124][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:59.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.144][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:31:59.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:31:59.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.157][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:59.160][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:31:59.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.164][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.167][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:59.170][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.175][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:31:59.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.189][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:59.192][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:59.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.197][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:59.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:31:59.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.213][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:59.216][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:59.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.224][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:31:59.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:31:59.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.235][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:59.237][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:59.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.242][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.245][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:31:59.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:31:59.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.255][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:59.258][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:59.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.263][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:31:59.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:31:59.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:59.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:59.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:59.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:59.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:31:59.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:31:59.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:31:59.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:31:59.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:59.372][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-08-01 00:31:59.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:31:59.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:31:59.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:31:59.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:31:59.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:59.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:59.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:59.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:59.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:59.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:59.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:59.431][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-08-01 00:31:59.434][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:31:59.438][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-08-01 00:31:59.441][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:31:59.443][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:31:59.446][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:31:59.448][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:31:59.450][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:31:59.451][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:31:59.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:31:59.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:31:59.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:31:59.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:31:59.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:31:59.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:31:59.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:31:59.481][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-08-01 00:31:59.488][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:31:59.490][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:31:59.493][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-08-01 00:31:59.875][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-08-01 00:32:00.260][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:00.264][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-08-01 00:32:00.272][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-08-01 00:32:00.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-08-01 00:32:00.282][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:32:00.285][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:32:00.288][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:32:00.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:00.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:00.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:00.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:00.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:00.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:00.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:00.316][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.323][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.335][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:00.337][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:00.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.342][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.344][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:00.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:00.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.367][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:00.370][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:00.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.375][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:00.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.388][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:00.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:00.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.392][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:00.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:00.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.402][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:00.404][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:00.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.407][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:00.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:00.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.417][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:00.419][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:00.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.424][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.427][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:00.430][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.434][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.436][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:00.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:00.443][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:00.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.446][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:00.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.456][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:00.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:00.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.463][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:00.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:00.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.474][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:00.477][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:00.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.482][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.484][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:00.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.493][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:00.494][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:00.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.498][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.500][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:00.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:00.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:00.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:00.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:00.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:00.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:00.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:00.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:00.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:00.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:00.622][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-08-01 00:32:00.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:00.682][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:00.689][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:00.692][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-01 00:32:00.695][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:00.698][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-01 00:32:00.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:00.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:00.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:00.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:00.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:00.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:00.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:00.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:00.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:00.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:00.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:00.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:00.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:00.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:00.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:00.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:00.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:00.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:00.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:01.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:01.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:01.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:01.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:01.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:01.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:01.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:01.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:01.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:01.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:01.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:02.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:02.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:02.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:02.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:02.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:02.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:02.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:02.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:02.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:02.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:02.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:02.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:02.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:02.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:02.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:02.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:02.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:02.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:02.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:02.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:02.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:02.185][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:02.192][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:02.195][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:02.199][private$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[2025-08-01 00:32:02.584][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[2025-08-01 00:32:02.967][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:02.972][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-08-01 00:32:02.982][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-08-01 00:32:02.990][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[2025-08-01 00:32:02.999][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:03.001][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:03.006][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:32:03.392][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:32:03.774][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:03.778][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-08-01 00:32:03.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-08-01 00:32:03.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:03.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:03.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:03.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:03.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:03.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:03.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:03.816][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-08-01 00:32:03.817][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:32:03.821][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-08-01 00:32:03.824][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:32:03.826][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:32:03.829][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:32:03.831][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:03.834][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:32:03.836][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:32:03.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:03.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:03.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:03.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:03.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:03.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:03.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:03.858][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-08-01 00:32:03.862][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:03.863][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:03.865][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-08-01 00:32:04.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-08-01 00:32:04.644][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:04.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-08-01 00:32:04.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-08-01 00:32:04.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-08-01 00:32:04.666][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:32:04.668][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:32:04.670][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:32:04.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:04.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:04.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:04.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:04.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:04.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:04.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:04.697][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.699][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.702][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.714][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:04.716][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:04.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.721][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.723][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:04.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:04.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.731][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:04.733][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:04.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.737][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:04.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.749][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:04.752][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:04.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.756][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:04.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:04.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.768][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:04.769][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:04.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.773][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:04.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:04.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.786][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:04.789][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:04.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.793][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.796][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:04.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:04.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.804][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:04.807][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:04.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.812][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:04.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:04.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.824][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:04.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:04.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.830][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.840][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:04.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:04.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.847][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:04.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:04.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.856][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:04.857][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:04.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.860][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.862][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:04.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:04.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.871][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:04.873][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:04.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.876][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.878][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:04.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:04.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:04.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:04.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:04.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:04.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:04.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:04.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:04.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:04.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:04.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:04.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:04.997][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-08-01 00:32:05.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:05.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:05.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:05.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:05.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:05.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:05.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:05.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:05.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:05.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:05.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:05.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:05.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:05.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:05.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:05.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:05.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:05.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:05.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:05.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:05.096][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-08-01 00:32:05.098][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:32:05.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-08-01 00:32:05.105][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:32:05.107][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:32:05.110][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:32:05.112][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:05.114][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:32:05.117][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:32:05.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:05.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:05.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:05.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:05.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:05.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:05.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:05.146][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-08-01 00:32:05.151][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:05.153][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:05.156][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-08-01 00:32:05.539][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-08-01 00:32:05.928][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:05.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-08-01 00:32:05.940][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-08-01 00:32:05.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-08-01 00:32:05.949][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:32:05.951][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:32:05.953][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:32:05.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:05.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:05.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:05.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:05.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:05.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:05.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:05.977][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:05.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:05.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:05.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:05.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:05.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:05.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:05.995][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:05.997][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:05.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.001][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.004][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:06.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:06.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.013][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:06.016][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:06.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:06.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.032][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:06.034][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:06.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.037][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:06.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:06.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.049][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:06.051][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:06.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.055][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:06.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:06.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.065][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:06.067][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:06.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.071][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.073][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:06.076][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:06.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.080][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.082][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:06.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:06.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.090][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.096][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.108][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:06.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:06.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:06.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:06.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:06.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:06.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.132][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.134][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:06.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:06.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.143][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:06.165][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:06.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.170][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.173][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:06.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:06.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:06.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:06.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:06.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:06.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:06.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:06.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:06.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:06.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:06.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:06.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:06.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:06.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:06.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:06.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:06.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:06.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:06.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:06.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:06.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.265][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-08-01 00:32:06.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.340][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:06.348][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:06.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-01 00:32:06.354][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:06.357][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-01 00:32:06.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:06.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:06.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:06.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:06.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:06.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:06.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:06.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:06.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:06.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:06.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:07.407][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:07.411][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-01 00:32:07.414][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:07.417][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-01 00:32:07.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:07.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:07.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:07.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:07.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:07.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:07.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:07.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:07.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:07.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:07.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:07.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:08.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.551][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-01 00:32:08.577][biodb::testThat]
biodb.INFO [2025-08-01 00:32:08.579][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-01 00:32:08.581][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:08.584][biodb::testThat]
biodb.TRACE[2025-08-01 00:32:08.590][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-01 00:32:08.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-01 00:32:08.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:08.725][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:08.737][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:08.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-01 00:32:08.743][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:08.746][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-01 00:32:08.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.811][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:08.818][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:08.822][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-01 00:32:08.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:08.828][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-01 00:32:08.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:08.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:08.933][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-01 00:32:08.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:08.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:08.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:08.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:08.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:08.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:08.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:08.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:08.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:08.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:08.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:08.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:08.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:08.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:08.995][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:08.997][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:08.999][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:09.001][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.003][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.006][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.010][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.023][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.028][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.032][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.034][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:09.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.084][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-01 00:32:09.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:09.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:09.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:09.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:09.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:09.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:09.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:09.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.123][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:09.125][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:09.127][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:09.129][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.131][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.134][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.138][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.140][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.142][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.146][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.148][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.151][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.160][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.162][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:09.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.192][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-01 00:32:09.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:09.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:09.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:09.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:09.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:09.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:09.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:09.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.235][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:09.237][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:09.239][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:09.241][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.243][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.246][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.250][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.252][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.255][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.259][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.261][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.264][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:09.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.269][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.273][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.275][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:09.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:09.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.298][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-01 00:32:09.299][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-01 00:32:09.301][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-01 00:32:09.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:09.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:09.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:09.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:09.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:09.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:09.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:09.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:09.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:09.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:09.512][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:09.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:09.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:09.528][private$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[2025-08-01 00:32:09.907][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[2025-08-01 00:32:10.289][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:10.293][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-08-01 00:32:10.302][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-08-01 00:32:10.309][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[2025-08-01 00:32:10.317][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:10.319][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:10.323][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:32:10.708][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:32:11.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:11.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-08-01 00:32:11.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-08-01 00:32:11.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:11.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:11.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:11.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:11.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:11.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:11.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:11.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:11.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:11.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:11.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:11.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:11.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:11.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:11.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:11.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:11.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:11.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:11.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:11.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:11.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:11.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:11.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:11.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:11.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:11.380][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-01 00:32:11.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:11.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:11.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:11.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:11.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:11.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:11.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:11.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.483][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.485][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:11.487][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:11.489][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:11.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.501][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.509][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.514][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.516][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.519][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.523][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.525][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:11.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.551][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-01 00:32:11.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:11.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:11.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:11.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:11.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:11.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:11.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:11.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.679][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.681][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:11.683][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:11.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:11.687][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.690][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.692][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.696][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.701][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.705][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.707][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.733][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.735][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.737][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.742][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.744][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:11.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.773][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-01 00:32:11.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:11.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:11.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:11.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:11.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:11.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:11.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:11.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.821][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.824][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:11.826][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:11.828][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:11.830][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.833][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.835][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.839][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.841][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.843][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.847][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.849][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.852][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:11.854][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.861][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.863][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:11.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:11.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.893][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-01 00:32:11.895][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-01 00:32:11.897][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-01 00:32:11.916][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:11.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:11.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-01 00:32:11.930][biodb::testThat]
biodb.INFO [2025-08-01 00:32:11.931][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-01 00:32:11.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:11.934][biodb::testThat]
biodb.TRACE[2025-08-01 00:32:11.940][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-01 00:32:11.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-01 00:32:11.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:11.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:11.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:11.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:11.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:11.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:11.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:12.024][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:12.040][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:12.043][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-01 00:32:12.046][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:12.049][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-01 00:32:12.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:12.105][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:12.112][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:12.114][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-01 00:32:12.117][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:12.119][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-01 00:32:12.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:12.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:12.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:12.219][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-01 00:32:12.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.263][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.265][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:12.267][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:12.270][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:12.272][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.274][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.281][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.284][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.291][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.294][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.296][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.306][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.338][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-01 00:32:12.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.380][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.382][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:12.384][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:12.386][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:12.388][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.390][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.396][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.398][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.400][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.405][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.407][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.409][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.411][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.413][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.416][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.419][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:12.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.448][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-01 00:32:12.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.490][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.493][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:12.495][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:12.497][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:12.498][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.500][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.504][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.509][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.513][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.518][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.522][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.527][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.529][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:12.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.559][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-01 00:32:12.561][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-01 00:32:12.563][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-01 00:32:12.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:12.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:12.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:12.657][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:12.659][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-01 00:32:12.662][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:12.664][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-01 00:32:12.670][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:12.678][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:12.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-01 00:32:12.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:12.686][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-01 00:32:12.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:12.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:12.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:12.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:12.835][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-01 00:32:12.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:12.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:12.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:12.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.899][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.901][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:12.903][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:12.904][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:12.907][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.909][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.917][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.919][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.924][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.927][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.929][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:12.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.940][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.942][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:12.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:12.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:12.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:12.973][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-01 00:32:12.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:12.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:12.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:12.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:12.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.026][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:13.029][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:13.031][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:13.033][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.034][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.041][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.044][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.050][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.052][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.054][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.059][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.082][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.084][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:13.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.114][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-01 00:32:13.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.157][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.160][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:13.162][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:13.164][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:13.167][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.173][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.175][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.180][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.182][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.184][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.188][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.190][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.193][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.195][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.197][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.202][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.204][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:13.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.235][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-01 00:32:13.237][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-01 00:32:13.239][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-01 00:32:13.280][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:13.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:13.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-01 00:32:13.298][biodb::testThat]
biodb.INFO [2025-08-01 00:32:13.301][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-01 00:32:13.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:13.306][biodb::testThat]
biodb.TRACE[2025-08-01 00:32:13.313][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-01 00:32:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-01 00:32:13.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:13.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:13.399][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:13.407][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:13.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-01 00:32:13.413][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:13.416][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-01 00:32:13.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:13.515][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:13.523][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:13.526][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-01 00:32:13.529][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:13.532][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-01 00:32:13.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:13.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:13.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:13.670][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-01 00:32:13.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.718][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.720][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:13.722][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:13.725][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:13.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.729][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.731][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.736][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.741][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.746][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.750][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.753][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.755][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.769][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.770][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:13.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.796][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-01 00:32:13.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.838][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.841][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:13.843][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:13.845][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:13.847][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.849][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.852][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.856][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.865][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.867][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.901][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.911][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.913][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.941][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-01 00:32:13.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:13.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:13.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:13.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:13.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:13.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:13.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:13.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:13.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:13.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.988][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:13.990][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:13.992][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:13.994][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:13.996][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:13.998][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.002][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.005][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.007][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.012][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.014][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.016][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.019][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.021][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.026][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.028][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:14.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.057][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-01 00:32:14.059][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-01 00:32:14.061][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-01 00:32:14.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:14.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:14.202][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:14.210][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:14.212][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-01 00:32:14.215][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:14.218][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-01 00:32:14.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:14.231][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:14.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-01 00:32:14.236][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:14.239][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-01 00:32:14.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:14.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:14.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:14.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:14.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:14.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:14.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:14.423][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-01 00:32:14.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:14.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.490][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.492][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:14.494][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:14.497][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:14.499][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.501][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.508][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.511][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.518][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.520][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.522][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.531][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.534][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:14.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.563][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-01 00:32:14.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:14.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.609][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:14.611][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:14.613][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:14.615][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.617][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.620][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.624][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.628][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.632][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.634][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.636][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.638][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.640][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.643][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.645][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:14.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.684][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-01 00:32:14.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:14.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.751][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-01 00:32:14.753][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-01 00:32:14.756][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-01 00:32:14.758][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.761][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.763][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.768][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.770][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.776][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.778][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.780][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-01 00:32:14.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.789][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-01 00:32:14.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:14.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:14.820][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-01 00:32:14.822][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-01 00:32:14.824][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-01 00:32:14.870][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:14.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-01 00:32:14.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:14.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-01 00:32:14.886][biodb::testThat]
biodb.INFO [2025-08-01 00:32:14.889][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-08-01 00:32:14.891][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:14.893][biodb::testThat]
biodb.DEBUG[2025-08-01 00:32:14.897][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-08-01 00:32:14.899][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:32:14.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-08-01 00:32:14.906][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:32:14.908][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:32:14.910][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:32:14.913][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:14.915][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:32:14.917][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:32:14.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:14.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:14.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:14.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:14.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:14.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:14.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:14.963][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-08-01 00:32:14.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:14.973][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:14.976][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-08-01 00:32:15.358][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-08-01 00:32:15.744][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:15.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-08-01 00:32:15.756][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-08-01 00:32:15.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-08-01 00:32:15.766][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:32:15.769][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:32:15.772][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:32:15.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:15.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:15.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:15.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:15.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:15.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:15.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:15.803][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.806][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.810][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.822][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:15.825][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:15.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.829][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.831][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:15.834][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:15.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.838][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.841][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:15.844][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:15.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.848][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.851][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:15.853][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:15.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.858][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.860][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:15.863][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:15.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.867][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.870][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:15.872][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:15.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.877][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.879][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:15.882][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:15.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.886][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.889][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:15.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:15.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.896][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.899][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:15.902][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:15.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.906][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.909][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:15.911][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:15.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.916][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:15.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:15.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:15.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:15.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:15.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:15.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:15.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:15.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:15.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:16.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:16.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:16.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:16.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:16.010][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-08-01 00:32:16.012][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-08-01 00:32:16.030][biodb::testThat]
biodb.INFO [2025-08-01 00:32:16.032][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-08-01 00:32:16.033][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:16.035][biodb::testThat]
biodb.DEBUG[2025-08-01 00:32:16.059][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-08-01 00:32:16.061][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-08-01 00:32:16.063][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-08-01 00:32:16.067][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-08-01 00:32:16.070][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2025-08-01 00:32:16.073][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2025-08-01 00:32:16.076][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:32:16.078][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:16.080][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:32:16.082][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:32:16.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:16.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:16.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:16.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:16.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:16.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:16.111][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[2025-08-01 00:32:16.113][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-08-01 00:32:16.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:16.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:16.124][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-08-01 00:32:16.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-08-01 00:32:16.892][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:16.896][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-08-01 00:32:16.904][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-08-01 00:32:16.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:16.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:16.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:16.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:16.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:16.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:16.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:16.932][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-08-01 00:32:16.939][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:16.942][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:16.945][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-08-01 00:32:17.328][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-08-01 00:32:17.712][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:17.716][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-08-01 00:32:17.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-08-01 00:32:17.731][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-08-01 00:32:17.735][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:32:17.737][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-08-01 00:32:17.740][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-08-01 00:32:17.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:17.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:17.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:17.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:17.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:17.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:17.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:17.769][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:17.771][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:17.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.775][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:17.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.788][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:17.814][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:17.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.818][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.821][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:17.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:17.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.828][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.831][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:17.834][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:17.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.838][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.841][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:17.844][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:17.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.848][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.850][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:17.853][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:17.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.857][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.860][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:17.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:17.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.867][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.870][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:17.872][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:17.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.877][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.879][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:17.882][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:17.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.886][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.889][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:17.891][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:17.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.896][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.898][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:17.901][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:17.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.905][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:17.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:17.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:17.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:17.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:17.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:17.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:17.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:17.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:17.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:17.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:17.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:17.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:17.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:17.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:17.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:17.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:17.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:17.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:17.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:17.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:17.997][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:17.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.004][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.016][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:18.018][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:18.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.023][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.026][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:18.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:18.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.035][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:18.038][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:18.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.042][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.045][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:18.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:18.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.054][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:18.056][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:18.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.061][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:18.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:18.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.073][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.080][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.092][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.094][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.101][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.112][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:18.114][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:18.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.119][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.122][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:18.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.136][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.140][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.152][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:18.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:18.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.159][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:18.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:18.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.171][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:18.173][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:18.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.177][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.180][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:18.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:18.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.189][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:18.192][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:18.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.196][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.199][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:18.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:18.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:18.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:18.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:18.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:18.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:18.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:18.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:18.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-01 00:32:18.302][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.304][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.309][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.321][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:18.323][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:18.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.328][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.331][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:18.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.341][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:18.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:18.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.348][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:18.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:18.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.359][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:18.362][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:18.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:18.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:18.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.377][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.380][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.384][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:18.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.395][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.397][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.401][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.404][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:18.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.413][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:18.415][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:18.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.419][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.422][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:18.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.431][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.434][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.438][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:18.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.450][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:18.452][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:18.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.456][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:18.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:18.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:18.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:18.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.474][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.477][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:18.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.487][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:18.489][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:18.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.493][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.496][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:18.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:18.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:18.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:18.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:18.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:18.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:18.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:18.655][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-08-01 00:32:18.657][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-08-01 00:32:18.659][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-08-01 00:32:18.688][biodb::testThat]
biodb.INFO [2025-08-01 00:32:18.690][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-08-01 00:32:18.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:18.694][biodb::testThat]
biodb.INFO [2025-08-01 00:32:18.752][biodb::testThat]
biodb.INFO [2025-08-01 00:32:18.754][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-08-01 00:32:18.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:18.758][biodb::testThat]
biodb.INFO [2025-08-01 00:32:18.777][biodb::testThat]
biodb.INFO [2025-08-01 00:32:18.779][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-08-01 00:32:18.781][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:18.783][biodb::testThat]
biodb.DEBUG[2025-08-01 00:32:18.789][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[2025-08-01 00:32:18.797][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:18.799][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:18.803][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:32:19.225][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:32:19.668][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:19.673][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-08-01 00:32:19.682][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-08-01 00:32:19.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:19.713][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:19.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:19.717][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:19.720][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:19.723][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:19.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:19.727][ef$get] fields variable is a list.
biodb.INFO [2025-08-01 00:32:19.730][biodb::testThat]
biodb.INFO [2025-08-01 00:32:19.732][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-08-01 00:32:19.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:19.737][biodb::testThat]
biodb.ERROR[2025-08-01 00:32:19.765][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-08-01 00:32:19.800][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-08-01 00:32:19.829][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-01 00:32:19.831][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-01 00:32:19.834][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-01 00:32:19.836][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-01 00:32:19.838][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:19.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:19.841][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:19.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:19.845][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-01 00:32:19.870][biodb::testContext]
biodb.INFO [2025-08-01 00:32:19.872][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:32:19.874][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-08-01 00:32:19.876][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:32:19.878][biodb::testContext]
biodb.INFO [2025-08-01 00:32:19.883][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:32:19.886][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-01 00:32:19.893][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:19.895][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-01 00:32:19.898][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-01 00:32:19.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:19.906][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-01 00:32:19.908][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-01 00:32:19.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:19.916][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-01 00:32:19.918][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-01 00:32:19.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:19.927][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-01 00:32:19.929][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-01 00:32:19.931][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-01 00:32:19.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:19.939][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-01 00:32:19.942][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-01 00:32:19.944][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-01 00:32:19.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:19.951][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-01 00:32:19.953][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-01 00:32:19.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:19.961][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-01 00:32:19.964][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-01 00:32:19.966][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-01 00:32:19.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.972][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[2025-08-01 00:32:19.975][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-01 00:32:19.977][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-01 00:32:19.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:19.985][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-01 00:32:19.987][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-01 00:32:19.990][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-01 00:32:19.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:19.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:19.996][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[2025-08-01 00:32:19.998][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:32:20.000][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-01 00:32:20.002][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-01 00:32:20.005][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-01 00:32:20.007][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-01 00:32:20.010][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-01 00:32:20.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.018][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-01 00:32:20.021][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-01 00:32:20.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.027][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[2025-08-01 00:32:20.029][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-01 00:32:20.031][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-01 00:32:20.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.039][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-01 00:32:20.042][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-01 00:32:20.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.050][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-01 00:32:20.052][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-01 00:32:20.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.061][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-01 00:32:20.063][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-01 00:32:20.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.071][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:32:20.073][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-01 00:32:20.091][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-01 00:32:20.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.100][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-01 00:32:20.102][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-01 00:32:20.104][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-01 00:32:20.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.110][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[2025-08-01 00:32:20.113][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-01 00:32:20.117][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.119][self$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[2025-08-01 00:32:20.122][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.124][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:20.126][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.128][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.135][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:32:20.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:20.139][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.142][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-01 00:32:20.144][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:20.146][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.148][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.151][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:20.151][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:20.151][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:20.151][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:32:20.151][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:32:20.153][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:20.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:20.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.168][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.170][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:20.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:20.175][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.177][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.180][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-01 00:32:20.184][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.186][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:32:20.188][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.191][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:20.193][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.195][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.198][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.203][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:32:20.205][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:20.207][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.209][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-01 00:32:20.211][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:20.213][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.215][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.218][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:20.218][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:20.218][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:20.218][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:32:20.218][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:32:20.220][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:20.223][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.227][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:20.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.249][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.251][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.253][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:20.258][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:20.260][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.262][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.265][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-01 00:32:20.269][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.271][self$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[2025-08-01 00:32:20.287][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:20.291][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.293][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.295][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.297][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.299][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:32:20.302][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:20.304][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.306][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-01 00:32:20.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:20.311][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.313][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.315][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.317][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:20.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:20.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.329][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.331][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.332][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:20.334][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:20.336][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.338][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.340][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-01 00:32:20.344][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.347][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:32:20.349][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.351][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:20.353][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.358][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.362][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.364][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:32:20.366][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:20.369][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.371][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-01 00:32:20.373][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:20.376][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.378][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:20.380][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:20.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:20.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:20.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:20.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:20.399][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.401][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:20.403][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:20.406][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:20.408][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:20.411][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:20.413][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.434][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[2025-08-01 00:32:20.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.462][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[2025-08-01 00:32:20.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.472][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[2025-08-01 00:32:20.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.482][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[2025-08-01 00:32:20.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.545][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[2025-08-01 00:32:20.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.552][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[2025-08-01 00:32:20.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.562][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[2025-08-01 00:32:20.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.583][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-01 00:32:20.586][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-01 00:32:20.589][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-01 00:32:20.593][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-01 00:32:20.596][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:32:20.599][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-01 00:32:20.602][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-01 00:32:20.606][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-01 00:32:20.608][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-01 00:32:20.611][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-01 00:32:20.615][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:32:20.617][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-01 00:32:20.621][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-01 00:32:20.624][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-01 00:32:20.628][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-01 00:32:20.631][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-01 00:32:20.634][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-01 00:32:20.638][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-01 00:32:20.641][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:32:20.645][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-01 00:32:20.648][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-01 00:32:20.651][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-01 00:32:20.654][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-01 00:32:20.657][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-01 00:32:20.661][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-01 00:32:20.664][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-01 00:32:20.667][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-01 00:32:20.671][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-01 00:32:20.674][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-01 00:32:20.676][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-01 00:32:20.679][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-01 00:32:20.682][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-01 00:32:20.685][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-01 00:32:20.688][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-01 00:32:20.692][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-01 00:32:20.695][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-01 00:32:20.697][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-01 00:32:20.700][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-01 00:32:20.703][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-01 00:32:20.706][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-01 00:32:20.709][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-01 00:32:20.711][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-01 00:32:20.714][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-01 00:32:20.717][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-01 00:32:20.721][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-01 00:32:20.723][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-01 00:32:20.725][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-01 00:32:20.727][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-01 00:32:20.729][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-01 00:32:20.732][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-01 00:32:20.735][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-01 00:32:20.739][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-01 00:32:20.742][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-01 00:32:20.745][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-01 00:32:20.749][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-01 00:32:20.752][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-01 00:32:20.756][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-01 00:32:20.759][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-01 00:32:20.762][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-01 00:32:20.765][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-01 00:32:20.768][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-01 00:32:20.772][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-01 00:32:20.775][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-01 00:32:20.778][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-01 00:32:20.782][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-01 00:32:20.785][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-01 00:32:20.788][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:32:20.792][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:32:20.795][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-01 00:32:20.798][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-01 00:32:20.801][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-01 00:32:20.805][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-01 00:32:20.808][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-01 00:32:20.811][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-01 00:32:20.814][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-01 00:32:20.816][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-01 00:32:20.819][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-01 00:32:20.823][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-01 00:32:20.826][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-01 00:32:20.828][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-01 00:32:20.830][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-01 00:32:20.833][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-01 00:32:20.836][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-01 00:32:20.850][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-01 00:32:20.853][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:32:20.856][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:20.857][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.861][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.864][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.DEBUG[2025-08-01 00:32:20.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:20.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:20.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:20.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:20.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:20.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:20.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:20.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:21.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:21.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:21.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:21.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:21.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:21.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:21.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:21.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:21.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:21.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:21.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:21.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:21.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:21.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:21.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:21.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:21.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:21.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:21.101][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-01 00:32:21.104][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-01 00:32:21.108][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:21.110][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-01 00:32:21.112][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:21.114][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:21.116][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:21.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:21.120][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:21.122][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-01 00:32:21.124][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-01 00:32:21.126][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:21.129][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:21.131][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-01 00:32:21.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-01 00:32:21.135][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-01 00:32:21.138][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:21.139][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:21.139][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:21.139][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:21.141][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-01 00:32:21.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:21.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:21.147][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:21.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:21.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:21.154][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:21.156][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:21.156][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-01 00:32:21.158][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:21.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:21.162][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:21.164][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-01 00:32:21.164][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-01 00:32:21.167][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:32:21.171][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:32:21.174][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-01 00:32:21.178][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:32:21.181][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:32:21.185][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:32:21.192][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-01 00:32:21.194][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-01 00:32:21.196][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-01 00:32:21.200][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-01 00:32:21.202][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:32:21.205][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:32:21.207][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-01 00:32:21.210][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-01 00:32:21.212][biodb::testThat]
biodb.INFO [2025-08-01 00:32:21.214][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-08-01 00:32:21.216][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:21.218][biodb::testThat]
biodb.DEBUG[2025-08-01 00:32:21.226][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.INFO [2025-08-01 00:32:21.233][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-08-01 00:32:21.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:21.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:21.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-08-01 00:32:21.619][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-08-01 00:32:22.090][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:22.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-08-01 00:32:22.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-08-01 00:32:22.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:22.121][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:22.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:22.128][private$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[2025-08-01 00:32:22.514][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[2025-08-01 00:32:22.897][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:22.900][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-08-01 00:32:22.909][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-08-01 00:32:22.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:22.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:22.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:22.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:22.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:22.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:22.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:22.937][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[2025-08-01 00:32:22.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:22.947][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:22.950][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:32:23.334][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:32:23.717][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:23.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-08-01 00:32:23.730][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-08-01 00:32:23.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:23.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:23.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:23.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:23.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:23.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:23.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:23.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:23.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:23.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:23.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:23.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:23.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:23.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:23.825][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:23.832][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:23.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-01 00:32:23.837][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:23.840][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-01 00:32:23.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:23.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:23.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:23.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:23.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:23.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:23.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:23.866][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:23.874][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:23.916][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-01 00:32:23.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:23.923][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-01 00:32:23.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:23.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:23.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:23.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:23.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:23.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:23.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:23.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:23.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:23.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:23.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:23.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:23.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:23.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:23.981][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:23.988][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:23.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-01 00:32:23.994][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:23.997][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-01 00:32:24.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:24.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:24.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:24.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:24.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:24.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:24.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:24.027][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:24.034][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:24.038][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-01 00:32:24.041][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:24.044][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-01 00:32:24.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:24.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:24.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:24.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:24.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:24.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:24.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:24.073][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:24.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:24.082][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:24.087][private$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[2025-08-01 00:32:24.470][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[2025-08-01 00:32:24.853][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:24.858][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-08-01 00:32:24.867][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-08-01 00:32:24.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:24.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:24.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:24.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:24.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:24.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:24.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-01 00:32:24.909][biodb::testThat]
biodb.INFO [2025-08-01 00:32:24.911][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-08-01 00:32:24.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:24.945][biodb::testThat]
biodb.DEBUG[2025-08-01 00:32:24.952][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[2025-08-01 00:32:24.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:24.963][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:24.968][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:32:25.352][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:32:25.733][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:25.737][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-08-01 00:32:25.747][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-08-01 00:32:25.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:25.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:25.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:25.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:25.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:25.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:25.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:25.780][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:25.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:25.789][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:25.794][private$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[2025-08-01 00:32:26.176][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[2025-08-01 00:32:26.556][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-08-01 00:32:26.559][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-08-01 00:32:26.563][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-08-01 00:32:26.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-08-01 00:32:26.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:26.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:26.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:26.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:26.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:26.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-01 00:32:26.682][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-01 00:32:26.685][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-01 00:32:26.687][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-01 00:32:26.690][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-01 00:32:26.692][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:26.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:26.696][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:26.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:26.701][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-01 00:32:26.710][biodb::testContext]
biodb.INFO [2025-08-01 00:32:26.713][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:32:26.715][biodb::testContext] Test context - Test web services
biodb.INFO [2025-08-01 00:32:26.717][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:32:26.719][biodb::testContext]
biodb.INFO [2025-08-01 00:32:26.723][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:32:26.727][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-01 00:32:26.735][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:26.736][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-01 00:32:26.739][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-01 00:32:26.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.747][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-01 00:32:26.749][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-01 00:32:26.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.756][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-01 00:32:26.759][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-01 00:32:26.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.765][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[2025-08-01 00:32:26.767][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-01 00:32:26.769][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-01 00:32:26.772][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-01 00:32:26.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.780][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-01 00:32:26.782][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-01 00:32:26.783][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-01 00:32:26.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.791][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-01 00:32:26.794][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-01 00:32:26.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.800][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-01 00:32:26.803][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-01 00:32:26.806][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-01 00:32:26.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.815][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-01 00:32:26.817][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-01 00:32:26.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.825][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-01 00:32:26.827][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-01 00:32:26.830][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-01 00:32:26.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.839][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:32:26.841][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-01 00:32:26.843][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-01 00:32:26.846][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-01 00:32:26.848][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-01 00:32:26.851][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-01 00:32:26.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.860][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-01 00:32:26.862][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-01 00:32:26.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.869][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-01 00:32:26.871][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-01 00:32:26.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.880][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-01 00:32:26.883][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-01 00:32:26.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.892][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-01 00:32:26.895][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-01 00:32:26.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.904][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-01 00:32:26.906][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-01 00:32:26.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.915][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:32:26.918][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-01 00:32:26.935][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-01 00:32:26.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.957][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-01 00:32:26.959][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-01 00:32:26.962][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-01 00:32:26.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:26.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:26.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:26.970][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-01 00:32:26.975][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:26.978][self$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[2025-08-01 00:32:26.981][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:26.985][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:26.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:26.990][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:26.993][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:26.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:26.999][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:32:27.002][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:27.005][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.008][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-01 00:32:27.010][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:27.013][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.015][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.018][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:27.018][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:27.018][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:27.018][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:32:27.018][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:32:27.021][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:27.024][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:27.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.033][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.036][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:27.039][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:27.040][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.042][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.045][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-01 00:32:27.047][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.048][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:32:27.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:27.054][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.058][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.060][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.064][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:32:27.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:27.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.069][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-01 00:32:27.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:27.071][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.075][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:27.075][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:27.075][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:27.075][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:32:27.075][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:32:27.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:27.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.082][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.084][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:27.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.090][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.092][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:27.096][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:27.098][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.101][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.104][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-01 00:32:27.108][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.111][self$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[2025-08-01 00:32:27.113][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:27.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.120][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.122][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.125][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.127][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:32:27.129][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:27.131][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.133][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-01 00:32:27.135][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:27.137][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.139][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.140][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:27.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.147][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:27.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.153][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.155][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:27.159][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:27.161][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.163][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.166][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-01 00:32:27.170][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.172][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:32:27.175][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.177][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:27.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.182][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.184][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.186][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.188][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:32:27.190][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:27.193][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.195][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-01 00:32:27.197][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:27.200][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.202][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.204][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.206][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:27.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:27.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:27.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:27.218][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.220][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.222][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:27.224][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:27.226][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.228][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:27.231][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:27.233][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.274][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.DEBUG[2025-08-01 00:32:27.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.408][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-01 00:32:27.411][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-01 00:32:27.415][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-01 00:32:27.418][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-01 00:32:27.421][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:32:27.424][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-01 00:32:27.428][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-01 00:32:27.431][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-01 00:32:27.434][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-01 00:32:27.437][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-01 00:32:27.441][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:32:27.444][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-01 00:32:27.448][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-01 00:32:27.451][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-01 00:32:27.455][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-01 00:32:27.458][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-01 00:32:27.462][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-01 00:32:27.465][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-01 00:32:27.469][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:32:27.472][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-01 00:32:27.476][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-01 00:32:27.479][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-01 00:32:27.483][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-01 00:32:27.486][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-01 00:32:27.490][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-01 00:32:27.493][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-01 00:32:27.496][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-01 00:32:27.500][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-01 00:32:27.503][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-01 00:32:27.506][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-01 00:32:27.509][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-01 00:32:27.512][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-01 00:32:27.515][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-01 00:32:27.519][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-01 00:32:27.522][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-01 00:32:27.525][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-01 00:32:27.528][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-01 00:32:27.531][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-01 00:32:27.534][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-01 00:32:27.537][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-01 00:32:27.541][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-01 00:32:27.544][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-01 00:32:27.547][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-01 00:32:27.551][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-01 00:32:27.554][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-01 00:32:27.557][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-01 00:32:27.560][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-01 00:32:27.563][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-01 00:32:27.566][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-01 00:32:27.570][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-01 00:32:27.573][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-01 00:32:27.575][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-01 00:32:27.579][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-01 00:32:27.582][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-01 00:32:27.585][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-01 00:32:27.589][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-01 00:32:27.592][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-01 00:32:27.595][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-01 00:32:27.598][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-01 00:32:27.602][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-01 00:32:27.605][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-01 00:32:27.609][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-01 00:32:27.612][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-01 00:32:27.616][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-01 00:32:27.619][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-01 00:32:27.623][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-01 00:32:27.626][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:32:27.630][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:32:27.633][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-01 00:32:27.637][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-01 00:32:27.640][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-01 00:32:27.644][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-01 00:32:27.647][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-01 00:32:27.650][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-01 00:32:27.654][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-01 00:32:27.657][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-01 00:32:27.660][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-01 00:32:27.664][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-01 00:32:27.667][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-01 00:32:27.671][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-01 00:32:27.674][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-01 00:32:27.678][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-01 00:32:27.681][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-01 00:32:27.685][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-01 00:32:27.689][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:32:27.692][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:27.694][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.698][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.717][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[2025-08-01 00:32:27.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.777][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[2025-08-01 00:32:27.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.853][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.DEBUG[2025-08-01 00:32:27.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:27.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:27.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:27.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:27.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:27.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:27.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:27.959][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-01 00:32:27.962][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-01 00:32:27.967][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:27.970][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:27.977][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:27.982][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.984][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-01 00:32:27.985][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-01 00:32:27.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:27.989][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:27.991][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-01 00:32:27.993][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-01 00:32:27.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-01 00:32:27.999][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:28.000][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:28.000][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:28.000][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:28.001][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-01 00:32:28.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:28.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:28.006][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:28.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:28.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:28.013][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:28.014][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:28.014][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-01 00:32:28.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:28.018][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:28.021][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:28.023][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-01 00:32:28.023][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-01 00:32:28.026][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:32:28.030][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:32:28.034][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-01 00:32:28.038][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:32:28.042][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:32:28.046][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:32:28.055][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-01 00:32:28.057][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-01 00:32:28.060][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-01 00:32:28.063][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-01 00:32:28.066][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:32:28.069][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:32:28.072][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-01 00:32:28.075][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-01 00:32:28.078][biodb::testThat]
biodb.INFO [2025-08-01 00:32:28.080][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-08-01 00:32:28.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:28.085][biodb::testThat]
biodb.DEBUG[2025-08-01 00:32:28.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-01 00:32:28.108][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:28.110][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:28.112][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-08-01 00:32:28.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-08-01 00:32:28.964][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:28.969][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-08-01 00:32:28.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-08-01 00:32:29.033][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[2025-08-01 00:32:29.041][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:29.043][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:29.046][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-01 00:32:29.431][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-01 00:32:29.813][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:29.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-08-01 00:32:29.827][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-08-01 00:32:29.845][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-01 00:32:29.848][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-01 00:32:29.850][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-01 00:32:29.852][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-01 00:32:29.854][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:29.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:29.858][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:29.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:29.862][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-01 00:32:29.871][biodb::testContext]
biodb.INFO [2025-08-01 00:32:29.874][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:32:29.876][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-08-01 00:32:29.878][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-01 00:32:29.880][biodb::testContext]
biodb.INFO [2025-08-01 00:32:29.884][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:32:29.888][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-01 00:32:29.895][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:29.897][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-01 00:32:29.900][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-01 00:32:29.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:29.908][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-01 00:32:29.911][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-01 00:32:29.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:29.918][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-01 00:32:29.921][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-01 00:32:29.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:29.928][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-01 00:32:29.930][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-01 00:32:29.932][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-01 00:32:29.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:29.938][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-01 00:32:29.941][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-01 00:32:29.943][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-01 00:32:29.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:29.951][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-01 00:32:29.953][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-01 00:32:29.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:29.961][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-01 00:32:29.964][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-01 00:32:29.966][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-01 00:32:29.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.972][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[2025-08-01 00:32:29.974][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-01 00:32:29.977][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-01 00:32:29.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:29.986][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-01 00:32:29.988][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-01 00:32:29.990][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-01 00:32:29.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:29.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:29.996][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[2025-08-01 00:32:29.998][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:32:30.001][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-01 00:32:30.004][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-01 00:32:30.006][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-01 00:32:30.009][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-01 00:32:30.011][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-01 00:32:30.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.021][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-01 00:32:30.023][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-01 00:32:30.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.032][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-01 00:32:30.033][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-01 00:32:30.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.039][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-01 00:32:30.041][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-01 00:32:30.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.047][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-01 00:32:30.049][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-01 00:32:30.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.058][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-01 00:32:30.061][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-01 00:32:30.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.069][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-01 00:32:30.071][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-01 00:32:30.088][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-01 00:32:30.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.097][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-01 00:32:30.099][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-01 00:32:30.102][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-01 00:32:30.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.107][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[2025-08-01 00:32:30.110][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-01 00:32:30.115][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.117][self$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[2025-08-01 00:32:30.119][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.122][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:30.124][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.129][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.134][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:32:30.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:30.139][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.141][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-01 00:32:30.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:30.145][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.148][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.150][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:30.150][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:30.150][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:30.150][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:32:30.150][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:32:30.152][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:30.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:30.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.165][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.168][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.170][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:30.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:30.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.174][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.177][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-01 00:32:30.180][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.181][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:32:30.184][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.186][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:30.188][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.190][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.194][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.197][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:32:30.199][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:30.201][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.204][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-01 00:32:30.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:30.209][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.211][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.213][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:30.213][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:30.213][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:30.213][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-01 00:32:30.213][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-01 00:32:30.216][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:30.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.220][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.222][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:30.225][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.227][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.229][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.230][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:30.232][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:30.234][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.236][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.239][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-01 00:32:30.242][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.244][self$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[2025-08-01 00:32:30.247][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.249][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:30.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.255][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.258][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.260][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-01 00:32:30.262][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:30.265][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.267][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-01 00:32:30.269][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:30.272][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.274][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.276][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.278][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:30.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.284][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:30.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.290][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.292][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:30.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:30.298][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.300][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.303][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-01 00:32:30.306][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.309][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-01 00:32:30.311][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:30.316][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.318][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.320][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.322][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.324][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-01 00:32:30.327][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:30.329][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.331][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-01 00:32:30.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:30.335][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.337][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:30.338][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.340][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-01 00:32:30.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:30.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:30.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:30.351][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:30.353][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.355][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:30.356][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:30.357][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:30.359][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-01 00:32:30.362][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:30.364][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.376][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[2025-08-01 00:32:30.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.460][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[2025-08-01 00:32:30.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.469][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[2025-08-01 00:32:30.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.539][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[2025-08-01 00:32:30.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.549][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[2025-08-01 00:32:30.551][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-01 00:32:30.554][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-01 00:32:30.557][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-01 00:32:30.560][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-01 00:32:30.564][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:32:30.567][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-01 00:32:30.570][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-01 00:32:30.573][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-01 00:32:30.576][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-01 00:32:30.579][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-01 00:32:30.582][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:32:30.586][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-01 00:32:30.589][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-01 00:32:30.592][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-01 00:32:30.594][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-01 00:32:30.597][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-01 00:32:30.599][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-01 00:32:30.602][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-01 00:32:30.605][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:32:30.608][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-01 00:32:30.611][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-01 00:32:30.614][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-01 00:32:30.617][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-01 00:32:30.620][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-01 00:32:30.622][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-01 00:32:30.623][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-01 00:32:30.625][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-01 00:32:30.627][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-01 00:32:30.629][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-01 00:32:30.631][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-01 00:32:30.634][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-01 00:32:30.637][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-01 00:32:30.641][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-01 00:32:30.643][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-01 00:32:30.646][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-01 00:32:30.649][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-01 00:32:30.652][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-01 00:32:30.656][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-01 00:32:30.659][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-01 00:32:30.662][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-01 00:32:30.666][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-01 00:32:30.669][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-01 00:32:30.673][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-01 00:32:30.676][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-01 00:32:30.680][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-01 00:32:30.683][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-01 00:32:30.686][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-01 00:32:30.689][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-01 00:32:30.691][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-01 00:32:30.694][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-01 00:32:30.696][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-01 00:32:30.698][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-01 00:32:30.701][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-01 00:32:30.704][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-01 00:32:30.708][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-01 00:32:30.710][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-01 00:32:30.713][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-01 00:32:30.715][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-01 00:32:30.719][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-01 00:32:30.722][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-01 00:32:30.725][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-01 00:32:30.728][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-01 00:32:30.731][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-01 00:32:30.735][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-01 00:32:30.738][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-01 00:32:30.741][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-01 00:32:30.744][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:32:30.748][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:32:30.751][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-01 00:32:30.755][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-01 00:32:30.758][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-01 00:32:30.761][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-01 00:32:30.764][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-01 00:32:30.768][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-01 00:32:30.771][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-01 00:32:30.774][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-01 00:32:30.778][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-01 00:32:30.781][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-01 00:32:30.784][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-01 00:32:30.787][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-01 00:32:30.790][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-01 00:32:30.793][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-01 00:32:30.796][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-01 00:32:30.799][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-01 00:32:30.803][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-01 00:32:30.805][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-01 00:32:30.807][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.809][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.957][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.DEBUG[2025-08-01 00:32:30.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:30.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:30.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:30.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:30.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:30.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:30.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:30.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:31.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:31.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:31.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:31.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:31.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:31.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:31.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:31.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:31.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:31.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:31.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:31.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:31.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:31.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-01 00:32:31.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:31.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:31.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:31.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:31.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:31.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:31.041][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-01 00:32:31.043][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-01 00:32:31.048][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:31.050][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-01 00:32:31.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:31.054][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-01 00:32:31.057][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:31.059][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-01 00:32:31.061][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:31.063][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-01 00:32:31.065][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-01 00:32:31.068][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-01 00:32:31.070][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:31.072][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-01 00:32:31.074][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-01 00:32:31.077][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-01 00:32:31.079][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-01 00:32:31.081][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-01 00:32:31.081][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-01 00:32:31.081][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-01 00:32:31.084][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-01 00:32:31.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:31.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:31.089][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-01 00:32:31.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-01 00:32:31.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-01 00:32:31.095][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-01 00:32:31.097][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:31.097][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-01 00:32:31.099][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-01 00:32:31.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-01 00:32:31.104][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-01 00:32:31.106][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-01 00:32:31.106][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-01 00:32:31.109][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-01 00:32:31.113][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-01 00:32:31.116][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-01 00:32:31.119][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-01 00:32:31.123][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-01 00:32:31.126][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-01 00:32:31.133][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-01 00:32:31.136][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-01 00:32:31.139][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-01 00:32:31.142][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-01 00:32:31.144][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:32:31.146][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-01 00:32:31.149][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-01 00:32:31.151][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-01 00:32:31.162][biodb::testThat]
biodb.INFO [2025-08-01 00:32:31.165][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-08-01 00:32:31.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-01 00:32:31.168][biodb::testThat]
biodb.DEBUG[2025-08-01 00:32:31.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-01 00:32:31.182][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:31.185][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-01 00:32:31.187][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:31.190][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-01 00:32:31.198][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-01 00:32:31.206][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-01 00:32:31.247][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-08-01 00:32:31.250][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-01 00:32:31.254][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-08-01 00:32:31.264][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-08-01 00:32:31.266][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-01 00:32:31.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-08-01 00:32:31.272][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-01 00:32:31.274][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-01 00:32:31.277][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-01 00:32:31.279][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-01 00:32:31.281][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-01 00:32:31.283][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-01 00:32:31.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:31.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:31.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:31.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:31.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:31.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:31.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-01 00:32:31.312][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-08-01 00:32:31.318][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-01 00:32:31.321][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-01 00:32:31.323][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-08-01 00:32:31.710][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-08-01 00:32:32.364][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-01 00:32:32.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-08-01 00:32:32.377][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-08-01 00:32:32.384][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-08-01 00:32:32.389][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-01 00:32:32.392][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-01 00:32:32.394][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-01 00:32:32.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-01 00:32:32.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:32.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:32.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:32.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:32.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:32.421][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.TRACE[2025-08-01 00:32:32.430][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.433][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.437][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.481][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:32.483][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:32.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.487][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.491][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-01 00:32:32.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-01 00:32:32.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.501][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:32.503][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:32.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.508][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.512][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-01 00:32:32.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-01 00:32:32.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.522][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-01 00:32:32.525][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-01 00:32:32.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.530][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.533][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-01 00:32:32.535][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-01 00:32:32.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.540][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.543][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:32.545][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:32.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.550][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.553][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:32.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-01 00:32:32.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.562][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:32.565][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:32.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.569][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.572][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-01 00:32:32.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-01 00:32:32.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.583][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:32.586][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:32.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.590][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:32.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-01 00:32:32.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.602][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:32.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:32.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.610][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-01 00:32:32.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-01 00:32:32.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.623][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:32.626][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:32.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.630][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.633][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-01 00:32:32.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-01 00:32:32.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.643][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:32.645][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:32.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.650][ef$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.653][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-01 00:32:32.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-01 00:32:32.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:32.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:32.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:32.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:32.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-01 00:32:32.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-01 00:32:32.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-01 00:32:32.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-01 00:32:32.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-01 00:32:32.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-01 00:32:32.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-01 00:32:32.855][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-08-01 00:32:32.864][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-01 00:32:32.868][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-01 00:32:32.870][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-01 00:32:32.872][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-01 00:32:32.875][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-01 00:32:32.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-01 00:32:32.879][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-01 00:32:32.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-01 00:32:32.883][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-01 00:32:32.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 38.814   1.915  75.132

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	4.412	1.239	6.645
ChebiEntry	0.632	0.020	0.723