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This page was generated on 2025-09-01 11:41 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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

Package 206/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_21
git_last_commit: b8d718f
git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for biodbChebi on kjohnson1

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: 2025-08-29 14:06:24 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 14:07:55 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 91.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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 2.665  1.147    5.38
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.14.0’
** 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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-08-29 14:07:21.630][biodb::testContext]
biodb.INFO [2025-08-29 14:07:21.634][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:21.635][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-08-29 14:07:21.636][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:21.637][biodb::testContext]
biodb.INFO [2025-08-29 14:07:21.645][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:21.648][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:21.658][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:21.660][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 14:07:21.661][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 14:07:21.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.664][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 14:07:21.687][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 14:07:21.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.691][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 14:07:21.692][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 14:07:21.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.696][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 14:07:21.696][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 14:07:21.697][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 14:07:21.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.700][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 14:07:21.702][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 14:07:21.704][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 14:07:21.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.708][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 14:07:21.709][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 14:07:21.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.714][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 14:07:21.716][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 14:07:21.717][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 14:07:21.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.720][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 14:07:21.721][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 14:07:21.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.725][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 14:07:21.726][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 14:07:21.727][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 14:07:21.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.730][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:21.731][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 14:07:21.732][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 14:07:21.732][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 14:07:21.733][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 14:07:21.734][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 14:07:21.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.737][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 14:07:21.738][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 14:07:21.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.741][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 14:07:21.743][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 14:07:21.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.748][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[2025-08-29 14:07:21.749][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 14:07:21.750][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 14:07:21.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.753][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 14:07:21.754][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 14:07:21.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.757][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 14:07:21.758][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 14:07:21.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.761][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:21.762][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 14:07:21.783][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 14:07:21.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.789][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 14:07:21.790][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 14:07:21.791][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 14:07:21.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.797][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 14:07:21.833][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.859][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 14:07:21.861][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.862][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:21.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.866][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.867][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.870][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:21.870][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:21.871][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.872][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 14:07:21.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:21.874][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.875][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.876][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:21.876][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:21.876][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:21.876][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:21.876][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:21.877][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:21.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.879][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:21.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.884][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:21.886][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:21.887][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.888][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.889][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 14:07:21.891][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.892][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:21.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.893][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:21.894][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.895][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.896][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.897][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.898][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:21.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:21.899][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.900][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 14:07:21.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:21.902][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.903][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.904][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:21.904][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:21.904][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:21.904][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:21.904][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:21.904][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:21.905][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.912][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:21.913][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.915][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.917][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.918][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:21.920][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:21.921][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.922][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.923][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 14:07:21.925][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.926][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 14:07:21.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.930][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:21.931][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.932][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.933][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.936][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:21.938][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:21.939][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.940][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 14:07:21.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:21.942][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.944][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.945][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:21.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.947][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:21.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.950][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.951][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.952][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:21.953][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:21.953][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.954][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.956][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 14:07:21.959][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.960][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:21.961][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.962][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:21.963][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.964][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.965][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.965][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.966][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:21.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:21.968][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.969][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 14:07:21.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:21.970][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:21.972][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.973][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:21.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.975][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:21.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:21.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:21.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:21.980][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.981][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:21.982][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:21.983][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:21.984][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:21.989][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:21.990][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:21.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:21.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:21.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:21.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:21.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:21.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:21.998][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[2025-08-29 14:07:21.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.016][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[2025-08-29 14:07:22.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.027][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[2025-08-29 14:07:22.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.030][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[2025-08-29 14:07:22.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.058][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[2025-08-29 14:07:22.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.075][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 14:07:22.081][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 14:07:22.082][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 14:07:22.084][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 14:07:22.086][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:22.087][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 14:07:22.089][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:22.090][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:22.092][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 14:07:22.095][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 14:07:22.097][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:22.099][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 14:07:22.100][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:22.102][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:22.103][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 14:07:22.104][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 14:07:22.105][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 14:07:22.107][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 14:07:22.108][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:22.109][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 14:07:22.111][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 14:07:22.112][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 14:07:22.113][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 14:07:22.114][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 14:07:22.115][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 14:07:22.117][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 14:07:22.118][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 14:07:22.119][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 14:07:22.121][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 14:07:22.123][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 14:07:22.125][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 14:07:22.126][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 14:07:22.128][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 14:07:22.129][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 14:07:22.131][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 14:07:22.133][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 14:07:22.135][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 14:07:22.136][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 14:07:22.138][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 14:07:22.139][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 14:07:22.141][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 14:07:22.142][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 14:07:22.144][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 14:07:22.145][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 14:07:22.147][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 14:07:22.148][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 14:07:22.150][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 14:07:22.153][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 14:07:22.156][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 14:07:22.158][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 14:07:22.159][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 14:07:22.161][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 14:07:22.162][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 14:07:22.163][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 14:07:22.168][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 14:07:22.171][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 14:07:22.174][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 14:07:22.175][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 14:07:22.177][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 14:07:22.178][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 14:07:22.179][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 14:07:22.181][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 14:07:22.182][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 14:07:22.183][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 14:07:22.185][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 14:07:22.186][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 14:07:22.187][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:22.189][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:22.190][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 14:07:22.191][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 14:07:22.193][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 14:07:22.194][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 14:07:22.196][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 14:07:22.197][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 14:07:22.198][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 14:07:22.199][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 14:07:22.200][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 14:07:22.202][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 14:07:22.203][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 14:07:22.204][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 14:07:22.205][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 14:07:22.207][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 14:07:22.209][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 14:07:22.215][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 14:07:22.217][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:22.222][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:22.223][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.225][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.253][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[2025-08-29 14:07:22.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.264][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[2025-08-29 14:07:22.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.296][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.DEBUG[2025-08-29 14:07:22.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.332][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[2025-08-29 14:07:22.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:22.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:22.342][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:22.357][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 14:07:22.359][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:22.361][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 14:07:22.363][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:22.365][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:22.366][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:22.367][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:22.368][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:22.369][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 14:07:22.370][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 14:07:22.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:22.371][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:22.372][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 14:07:22.373][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 14:07:22.374][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 14:07:22.375][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:22.376][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:22.376][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:22.376][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:22.377][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 14:07:22.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:22.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:22.379][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:22.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:22.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:22.385][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:22.386][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:22.386][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 14:07:22.387][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:22.388][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:22.389][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:22.390][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 14:07:22.390][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 14:07:22.397][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:22.399][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:22.400][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 14:07:22.401][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:22.403][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:22.404][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:22.482][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 14:07:22.485][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 14:07:22.490][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 14:07:22.495][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 14:07:22.501][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:22.502][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:22.503][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 14:07:22.505][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 14:07:22.518][biodb::testThat]
biodb.INFO [2025-08-29 14:07:22.520][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-29 14:07:22.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:22.522][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:22.529][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-08-29 14:07:22.531][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:22.535][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:22.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:22.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:22.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:22.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:22.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:22.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:22.573][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.TRACE[2025-08-29 14:07:22.586][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.587][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.589][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.609][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:22.610][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:22.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.612][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.639][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:22.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:22.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.643][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:22.644][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:22.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.646][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:22.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:22.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.655][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:22.657][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:22.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.659][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:22.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:22.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.664][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.665][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.666][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.672][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:22.673][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:22.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.674][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.676][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:22.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:22.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.680][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:22.681][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:22.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.683][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.684][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:22.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:22.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.688][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:22.689][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:22.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.690][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:22.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:22.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.711][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:22.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:22.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.714][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.716][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:22.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:22.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.720][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:22.721][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:22.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.722][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.723][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:22.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:22.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.727][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:22.728][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:22.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.730][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.731][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:22.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:22.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:22.815][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-08-29 14:07:22.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:22.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:22.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:22.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:22.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:22.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:22.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:22.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:22.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:22.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.886][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 14:07:22.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 14:07:22.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.889][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 14:07:22.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 14:07:22.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.893][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 14:07:22.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 14:07:22.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.896][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 14:07:22.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 14:07:22.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:22.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:22.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:22.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:22.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:22.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.015][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.016][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.018][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.059][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.089][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.090][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.096][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.113][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.120][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.127][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.128][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.130][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.132][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.160][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.161][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.163][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.196][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.197][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.198][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.211][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.229][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.232][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.233][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.235][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.236][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.248][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.252][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.256][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.263][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.264][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.266][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.267][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.280][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.286][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.290][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.294][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.296][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.299][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.300][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.313][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.321][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.326][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.327][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.329][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.330][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.357][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.359][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.360][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.396][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.398][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.401][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.417][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.419][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.421][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.428][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.431][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.433][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.438][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.440][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.442][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.451][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.453][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.454][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.462][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.464][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.467][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.472][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.475][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.481][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.482][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.484][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.490][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.491][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.493][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.498][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.499][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.501][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.506][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.507][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.509][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.517][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.518][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.520][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:23.529][biodb::testThat]
biodb.INFO [2025-08-29 14:07:23.530][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-29 14:07:23.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:23.532][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:23.550][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-08-29 14:07:23.560][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:23.566][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-08-29 14:07:23.568][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:23.571][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-08-29 14:07:23.574][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:23.610][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:23.612][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:23.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:23.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:23.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:23.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:23.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:23.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:23.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:23.627][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.629][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.652][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.654][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.656][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.658][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:23.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:23.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.663][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.664][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.665][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.666][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:23.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:23.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.670][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.671][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.672][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:23.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:23.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.677][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.678][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.679][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:23.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.687][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.688][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.690][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.691][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:23.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.695][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:23.696][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.697][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.698][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:23.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:23.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.702][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.703][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.704][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:23.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.709][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.711][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.716][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:23.717][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.718][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.719][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:23.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:23.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.730][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.732][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:23.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:23.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:23.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:23.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:23.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:23.785][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-08-29 14:07:23.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-29 14:07:23.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-29 14:07:23.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-29 14:07:23.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-29 14:07:23.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-29 14:07:23.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-29 14:07:23.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:23.805][biodb::testThat]
biodb.INFO [2025-08-29 14:07:23.807][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-29 14:07:23.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:23.808][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:23.811][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.814][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:23.816][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-08-29 14:07:23.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:23.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:23.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:23.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:23.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:23.871][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-08-29 14:07:23.877][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 14:07:23.911][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:23.935][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 14:07:23.937][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:23.939][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 14:07:23.963][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[2025-08-29 14:07:23.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:23.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:23.972][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 14:07:24.257][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 14:07:24.412][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:24.415][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-08-29 14:07:24.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-08-29 14:07:24.434][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-08-29 14:07:24.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:24.457][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:24.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.458][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.459][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.460][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.462][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:24.467][biodb::testThat]
biodb.INFO [2025-08-29 14:07:24.468][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-29 14:07:24.469][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:24.470][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:24.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:24.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:24.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:24.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:24.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:24.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:24.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:24.589][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:24.594][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:24.596][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 14:07:24.597][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:24.598][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-08-29 14:07:24.626][biodb::testThat]
biodb.INFO [2025-08-29 14:07:24.627][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-29 14:07:24.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:24.628][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:24.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:24.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:24.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:24.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:24.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.683][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.692][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 14:07:24.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 14:07:24.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 14:07:24.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 14:07:24.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:24.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:24.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:24.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:24.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:24.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 14:07:24.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.761][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 14:07:24.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 14:07:24.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:24.765][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 14:07:24.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 14:07:24.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:24.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:24.780][biodb::testThat]
biodb.INFO [2025-08-29 14:07:24.781][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-29 14:07:24.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:24.783][biodb::testThat]
biodb.INFO [2025-08-29 14:07:24.795][biodb::testThat]
biodb.INFO [2025-08-29 14:07:24.797][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-29 14:07:24.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:24.799][biodb::testThat]
biodb.INFO [2025-08-29 14:07:24.809][biodb::testThat]
biodb.INFO [2025-08-29 14:07:24.810][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-29 14:07:24.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:24.812][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:24.816][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-08-29 14:07:25.023][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-08-29 14:07:25.250][biodb::testThat]
biodb.INFO [2025-08-29 14:07:25.251][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-29 14:07:25.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:25.253][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:25.344][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[2025-08-29 14:07:25.444][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:25.446][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:25.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.448][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:25.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:25.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.451][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:25.454][biodb::testThat]
biodb.INFO [2025-08-29 14:07:25.456][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-08-29 14:07:25.457][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:25.460][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:25.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:25.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:25.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:25.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:25.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:25.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:25.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:25.595][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:25.599][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:25.601][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 14:07:25.602][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:25.604][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 14:07:25.695][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:25.699][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:25.701][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 14:07:25.702][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:25.703][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-08-29 14:07:25.722][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 14:07:25.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 14:07:25.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:25.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:25.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:25.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:25.780][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:25.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:25.802][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:25.820][private$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[2025-08-29 14:07:25.900][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[2025-08-29 14:07:25.979][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:25.983][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-08-29 14:07:25.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-08-29 14:07:25.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:25.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:25.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:25.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:25.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:26.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:26.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:26.005][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-08-29 14:07:26.067][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:26.069][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-08-29 14:07:26.071][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:26.072][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:26.073][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:26.074][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:26.075][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:26.076][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:26.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:26.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:26.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:26.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:26.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:26.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:26.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:26.090][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-08-29 14:07:26.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:26.095][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:26.096][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-08-29 14:07:26.183][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-08-29 14:07:26.258][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:26.261][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-08-29 14:07:26.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-08-29 14:07:26.271][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-08-29 14:07:26.273][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:26.274][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:26.275][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:26.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:26.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:26.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:26.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:26.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:26.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:26.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:26.305][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.306][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.308][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.313][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:26.314][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:26.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.316][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:26.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:26.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.321][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:26.322][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:26.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.323][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.325][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:26.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:26.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.330][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:26.331][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:26.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.333][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:26.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:26.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.340][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:26.341][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:26.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.344][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:26.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:26.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.352][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:26.354][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:26.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.355][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.357][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:26.358][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.360][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.361][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:26.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:26.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:26.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.367][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:26.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:26.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.372][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:26.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:26.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.374][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:26.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:26.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.379][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:26.380][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:26.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.382][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.383][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:26.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:26.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.387][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:26.388][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:26.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.389][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.390][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:26.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:26.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:26.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:26.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:26.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:26.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:26.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:26.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:26.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:26.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:26.445][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-08-29 14:07:26.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:26.474][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[2025-08-29 14:07:26.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:26.479][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:26.481][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 14:07:26.561][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 14:07:26.642][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:26.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-08-29 14:07:26.651][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-08-29 14:07:26.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:26.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:26.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:26.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:26.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:26.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:26.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:26.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:26.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:26.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:26.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:26.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:26.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:26.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:26.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:26.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:26.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:26.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:26.726][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-08-29 14:07:26.728][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:26.729][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-08-29 14:07:26.731][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:26.732][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:26.733][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:26.734][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:26.735][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:26.736][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:26.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:26.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:26.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:26.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:26.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:26.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:26.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:26.766][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-08-29 14:07:26.771][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:26.772][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-08-29 14:07:26.774][rule$waitAsNeeded] Wait 0.0455399 second(s).
biodb.TRACE[2025-08-29 14:07:26.972][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-08-29 14:07:27.069][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-08-29 14:07:27.148][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:27.151][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-08-29 14:07:27.155][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-08-29 14:07:27.160][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-08-29 14:07:27.163][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:27.164][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:27.165][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:27.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:27.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:27.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:27.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:27.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:27.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:27.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:27.192][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.194][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.197][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.202][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:27.202][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:27.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.204][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.205][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:27.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:27.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.209][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:27.210][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:27.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.214][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:27.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:27.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:27.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:27.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.225][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:27.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.229][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:27.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:27.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.232][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:27.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:27.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.237][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:27.237][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:27.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.239][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.240][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:27.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.243][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.244][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:27.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:27.250][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:27.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.252][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:27.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:27.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.258][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:27.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:27.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.260][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:27.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:27.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:27.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:27.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.268][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.269][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.274][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:27.275][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:27.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.277][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:27.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:27.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:27.382][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-08-29 14:07:27.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:27.418][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[2025-08-29 14:07:27.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:27.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 14:07:27.425][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:27.426][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 14:07:27.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:27.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:27.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:27.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:27.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:27.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:27.442][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[2025-08-29 14:07:27.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:27.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:27.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:27.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:27.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:27.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:27.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:27.472][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[2025-08-29 14:07:27.473][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-08-29 14:07:27.474][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:27.477][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-08-29 14:07:27.479][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:27.481][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:27.482][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:27.483][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:27.484][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:27.485][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:27.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:27.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:27.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:27.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:27.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:27.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:27.500][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[2025-08-29 14:07:27.501][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-08-29 14:07:27.504][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:27.506][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:27.507][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-08-29 14:07:27.592][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-08-29 14:07:27.668][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:27.672][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-08-29 14:07:27.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-08-29 14:07:27.681][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-08-29 14:07:27.684][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:27.685][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:27.687][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:27.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:27.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:27.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:27.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:27.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:27.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:27.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:27.706][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.707][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.710][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.715][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:27.716][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:27.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.719][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.721][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:27.722][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:27.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.725][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.726][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:27.727][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:27.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.730][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.732][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:27.734][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:27.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.738][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.739][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:27.740][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:27.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.755][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.757][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:27.758][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.760][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.761][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:27.762][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:27.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.764][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.765][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:27.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:27.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.767][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:27.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:27.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:27.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:27.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.777][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.779][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:27.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.782][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:27.783][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:27.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.785][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:27.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:27.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:27.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:27.832][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-08-29 14:07:27.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:27.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:27.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:27.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:27.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:27.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:27.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:27.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:27.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:27.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:27.878][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[2025-08-29 14:07:27.879][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-08-29 14:07:27.880][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:27.881][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-08-29 14:07:27.883][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:27.884][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:27.885][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:27.886][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:27.887][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:27.887][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:27.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:27.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:27.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:27.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:27.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:27.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:27.906][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[2025-08-29 14:07:27.908][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-08-29 14:07:27.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:27.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:27.915][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-08-29 14:07:28.002][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-08-29 14:07:28.088][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:28.091][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-08-29 14:07:28.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-08-29 14:07:28.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-08-29 14:07:28.101][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:28.102][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:28.103][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:28.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:28.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:28.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:28.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:28.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:28.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:28.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:28.119][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.120][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.124][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.131][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:28.132][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:28.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.134][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.135][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:28.137][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:28.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.139][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.140][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:28.142][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:28.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.144][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.145][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.146][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.148][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.151][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.153][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.154][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.156][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:28.157][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.158][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.159][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.160][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.176][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.178][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:28.179][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:28.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.181][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:28.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.188][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:28.189][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:28.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.190][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.192][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:28.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:28.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.195][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:28.196][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:28.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.198][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:28.241][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-08-29 14:07:28.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:28.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:28.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:28.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:28.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:28.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:28.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:28.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:28.274][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-08-29 14:07:28.285][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:28.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-08-29 14:07:28.289][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:28.290][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:28.291][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:28.292][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:28.293][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:28.294][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:28.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:28.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:28.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:28.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:28.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:28.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:28.310][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[2025-08-29 14:07:28.311][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-08-29 14:07:28.314][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:28.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:28.317][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-08-29 14:07:28.403][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-08-29 14:07:28.482][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:28.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-08-29 14:07:28.490][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-08-29 14:07:28.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-08-29 14:07:28.495][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:28.497][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:28.498][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:28.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:28.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:28.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:28.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:28.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:28.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:28.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:28.514][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.515][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.517][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.522][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:28.522][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:28.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.524][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.525][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:28.526][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:28.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.528][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.529][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:28.530][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:28.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.532][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.533][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.534][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.536][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.537][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.538][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.540][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.541][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:28.542][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.544][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.545][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.547][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.550][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.551][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:28.552][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:28.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.555][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:28.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:28.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.576][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:28.577][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:28.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.578][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.579][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:28.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:28.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.584][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:28.585][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:28.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.586][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:28.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:28.625][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-08-29 14:07:28.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:28.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:28.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:28.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:28.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:28.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:28.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:28.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:28.654][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-08-29 14:07:28.655][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:28.657][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-08-29 14:07:28.658][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:28.659][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:28.660][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:28.661][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:28.670][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:28.671][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:28.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:28.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:28.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:28.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:28.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:28.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:28.685][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[2025-08-29 14:07:28.686][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-08-29 14:07:28.689][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:28.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:28.692][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-08-29 14:07:28.779][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-08-29 14:07:28.862][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:28.864][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-08-29 14:07:28.868][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-08-29 14:07:28.871][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-08-29 14:07:28.873][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:28.874][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:28.875][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:28.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:28.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:28.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:28.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:28.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:28.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:28.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:28.891][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.892][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.894][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:28.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:28.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.903][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:28.904][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:28.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.906][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.908][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:28.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:28.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.914][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:28.915][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:28.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.918][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.919][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:28.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:28.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.926][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:28.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:28.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.930][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:28.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:28.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.934][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.935][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.939][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:28.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.946][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.947][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.949][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.951][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:28.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.968][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:28.970][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.973][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.974][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:28.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:28.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.979][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.980][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:28.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.992][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:28.993][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:28.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:28.994][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:28.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:28.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.001][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:29.002][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:29.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.003][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.004][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:29.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:29.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.009][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:29.010][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:29.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.012][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.013][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:29.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:29.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:29.058][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-08-29 14:07:29.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:29.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:29.095][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-08-29 14:07:29.096][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:29.098][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-08-29 14:07:29.099][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:29.101][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:29.102][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:29.103][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:29.104][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:29.105][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:29.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:29.122][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-08-29 14:07:29.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:29.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:29.129][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-08-29 14:07:29.222][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-08-29 14:07:29.299][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:29.302][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-08-29 14:07:29.306][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-08-29 14:07:29.308][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-08-29 14:07:29.310][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:29.312][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:29.319][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:29.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:29.335][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.336][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.338][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.342][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:29.343][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:29.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.346][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.348][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:29.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.351][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:29.352][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:29.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.356][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:29.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:29.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.365][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:29.366][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:29.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.368][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:29.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.383][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.384][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.386][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.391][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:29.391][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:29.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.393][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.394][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:29.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:29.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.398][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:29.399][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.400][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.402][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:29.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.405][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.406][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.408][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.417][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:29.419][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:29.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.421][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:29.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:29.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.427][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:29.428][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:29.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.429][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.430][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:29.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:29.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.434][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:29.435][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:29.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.437][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.438][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:29.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:29.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:29.485][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-08-29 14:07:29.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:29.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:29.509][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-08-29 14:07:29.510][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:29.512][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-08-29 14:07:29.513][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:29.514][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:29.515][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:29.516][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:29.517][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:29.518][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:29.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:29.536][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-08-29 14:07:29.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:29.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:29.541][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-08-29 14:07:29.625][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-08-29 14:07:29.706][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:29.707][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-08-29 14:07:29.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-08-29 14:07:29.712][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-08-29 14:07:29.713][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:29.713][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:29.714][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:29.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:29.724][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.725][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.728][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.734][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:29.735][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:29.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.736][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.750][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:29.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:29.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.754][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:29.756][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:29.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.757][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:29.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:29.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.759][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:29.759][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:29.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.760][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:29.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:29.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.762][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.763][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.763][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:29.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.766][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:29.767][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:29.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.768][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.769][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:29.769][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.770][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.770][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:29.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.775][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.777][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:29.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.784][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:29.786][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:29.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:29.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.789][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:29.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:29.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.790][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.795][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:29.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:29.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.801][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:29.802][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:29.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.803][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.805][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:29.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:29.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:29.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:29.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:29.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:29.855][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-08-29 14:07:29.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:29.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:29.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:29.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:29.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:29.876][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-08-29 14:07:29.876][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:29.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-08-29 14:07:29.881][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:29.881][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:29.882][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:29.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:29.884][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:29.884][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:29.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:29.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:29.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:29.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:29.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:29.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:29.897][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[2025-08-29 14:07:29.898][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-08-29 14:07:29.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:29.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:29.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-08-29 14:07:29.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-08-29 14:07:30.054][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:30.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-08-29 14:07:30.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-08-29 14:07:30.060][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-08-29 14:07:30.061][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:30.061][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:30.062][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:30.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:30.084][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.087][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.092][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:30.093][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:30.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.095][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.096][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:30.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:30.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.100][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:30.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:30.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.102][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:30.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:30.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.109][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:30.111][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:30.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:30.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:30.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.121][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.122][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.124][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.128][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:30.129][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:30.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.131][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.132][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:30.133][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.135][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.136][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:30.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.142][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.144][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:30.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:30.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.145][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:30.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:30.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.147][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:30.148][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:30.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.148][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.149][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:30.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:30.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.150][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:30.153][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:30.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.155][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.156][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:30.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:30.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:30.194][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-08-29 14:07:30.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:30.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.206][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[2025-08-29 14:07:30.207][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-08-29 14:07:30.207][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:30.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-08-29 14:07:30.208][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:30.209][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:30.209][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:30.210][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:30.210][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:30.210][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:30.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:30.218][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-08-29 14:07:30.219][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:30.220][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:30.221][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-08-29 14:07:30.298][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-08-29 14:07:30.367][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:30.369][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-08-29 14:07:30.384][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-08-29 14:07:30.388][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-08-29 14:07:30.389][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:30.391][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:30.392][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:30.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:30.409][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.410][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.412][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.417][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:30.419][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:30.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.422][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.423][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:30.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:30.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.425][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:30.426][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:30.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.426][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.427][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:30.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:30.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.428][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:30.431][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:30.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.433][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:30.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:30.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.439][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.440][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.442][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.446][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:30.447][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:30.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.449][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.450][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:30.451][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.454][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.454][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.456][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.456][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.457][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.459][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:30.460][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:30.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.460][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:30.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:30.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.463][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:30.464][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:30.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.465][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:30.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:30.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.480][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:30.481][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:30.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.482][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:30.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:30.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:30.529][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-08-29 14:07:30.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:30.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:30.541][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-08-29 14:07:30.541][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:30.542][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-08-29 14:07:30.543][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:30.543][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:30.544][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:30.544][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:30.545][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:30.545][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:30.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:30.567][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-08-29 14:07:30.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:30.572][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:30.574][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-08-29 14:07:30.656][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-08-29 14:07:30.731][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:30.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-08-29 14:07:30.740][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-08-29 14:07:30.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-08-29 14:07:30.746][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:30.747][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:30.748][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:30.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:30.763][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.765][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.771][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:30.773][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:30.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.774][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.776][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:30.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:30.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.779][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:30.780][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:30.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.781][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:30.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:30.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.786][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:30.787][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:30.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.788][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:30.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:30.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.793][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.794][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.795][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:30.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.800][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:30.801][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:30.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.803][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.805][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:30.809][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.811][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.812][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:30.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.821][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:30.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.837][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:30.838][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:30.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.840][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:30.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:30.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.846][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:30.847][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:30.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.851][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.853][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:30.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:30.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.857][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:30.858][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:30.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.860][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:30.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:30.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:30.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:30.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:30.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:30.903][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-08-29 14:07:30.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:30.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:30.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.928][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[2025-08-29 14:07:30.929][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-08-29 14:07:30.938][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:30.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-08-29 14:07:30.943][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:30.945][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:30.947][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:30.948][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:30.949][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:30.950][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:30.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:30.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:30.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:30.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:30.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:30.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:30.968][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[2025-08-29 14:07:30.970][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-08-29 14:07:30.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:30.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:30.975][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-08-29 14:07:31.055][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-08-29 14:07:31.138][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:31.141][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-08-29 14:07:31.147][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-08-29 14:07:31.151][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-08-29 14:07:31.153][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:31.154][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:31.155][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:31.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:31.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:31.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:31.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:31.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:31.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:31.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:31.170][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.172][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.175][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.180][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:31.181][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:31.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.182][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.184][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:31.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:31.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.190][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:31.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:31.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.193][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.194][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:31.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:31.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.198][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:31.200][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:31.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.203][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.205][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:31.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:31.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.209][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:31.209][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:31.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.211][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:31.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:31.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.232][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:31.234][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:31.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.236][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.238][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:31.239][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.240][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.241][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:31.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.248][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.252][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:31.253][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:31.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.255][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.260][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:31.262][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:31.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.267][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.269][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:31.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:31.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.273][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:31.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:31.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.275][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.276][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:31.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:31.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:31.322][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-08-29 14:07:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:31.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:31.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:31.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:31.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:31.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:31.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:31.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:31.358][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-08-29 14:07:31.359][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:31.360][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-08-29 14:07:31.362][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:31.363][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:31.364][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:31.365][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:31.368][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:31.369][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:31.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:31.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:31.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:31.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:31.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:31.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:31.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:31.386][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-08-29 14:07:31.388][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:31.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:31.391][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-08-29 14:07:31.467][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-08-29 14:07:31.544][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:31.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-08-29 14:07:31.553][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-08-29 14:07:31.556][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-08-29 14:07:31.558][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:31.559][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:31.560][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:31.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:31.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:31.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:31.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:31.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:31.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:31.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:31.576][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.577][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.579][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.587][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:31.588][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:31.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.590][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.592][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.596][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:31.597][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:31.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.599][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.600][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:31.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:31.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.604][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:31.618][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:31.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.622][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.624][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:31.625][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:31.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.627][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.628][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:31.629][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:31.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.631][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.632][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:31.633][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.635][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.636][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:31.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.642][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.643][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.645][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:31.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.653][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:31.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:31.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.658][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:31.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:31.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.664][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:31.665][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:31.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.667][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.668][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:31.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:31.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.671][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:31.672][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:31.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.674][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:31.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:31.714][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-08-29 14:07:31.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:31.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:31.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:31.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:31.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:31.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:31.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:31.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:31.746][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[2025-08-29 14:07:31.748][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-08-29 14:07:31.750][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:31.751][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-08-29 14:07:31.753][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:31.754][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:31.755][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:31.756][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:31.757][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:31.758][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:31.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:31.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:31.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:31.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:31.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:31.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:31.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:31.778][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-08-29 14:07:31.783][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:31.784][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:31.786][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-08-29 14:07:31.863][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-08-29 14:07:31.940][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:31.943][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-08-29 14:07:31.947][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-08-29 14:07:31.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-08-29 14:07:31.952][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:31.954][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:31.955][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:31.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:31.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:31.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:31.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:31.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:31.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:31.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:31.971][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.972][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.974][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:31.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:31.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.979][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:31.980][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:31.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.985][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:31.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:31.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.989][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:31.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:31.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:31.992][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:31.993][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:31.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:31.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.010][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:32.012][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:32.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.014][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.016][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.018][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.019][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:32.020][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:32.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.022][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.023][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:32.024][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.025][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.026][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:32.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.030][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.034][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.037][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.042][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:32.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:32.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.045][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:32.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:32.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.050][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:32.050][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:32.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.052][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.053][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:32.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:32.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.057][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:32.059][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:32.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.060][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:32.107][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-08-29 14:07:32.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:32.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:32.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:32.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:32.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:32.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:32.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:32.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:32.148][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-08-29 14:07:32.151][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:32.154][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-08-29 14:07:32.156][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:32.157][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:32.159][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:32.161][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:32.162][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:32.163][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:32.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:32.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:32.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:32.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:32.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:32.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:32.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:32.180][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-08-29 14:07:32.184][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:32.185][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:32.187][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-08-29 14:07:32.270][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-08-29 14:07:32.352][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:32.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-08-29 14:07:32.358][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-08-29 14:07:32.361][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-08-29 14:07:32.363][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:32.365][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:32.366][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:32.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:32.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:32.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:32.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:32.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:32.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:32.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:32.383][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.386][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.390][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:32.391][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:32.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.393][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.394][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:32.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:32.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.398][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:32.398][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:32.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.400][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:32.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:32.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.422][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:32.423][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:32.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.425][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:32.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:32.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.429][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.430][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.432][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.437][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:32.438][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:32.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.441][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.443][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:32.444][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.446][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.448][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:32.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.452][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.453][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.455][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.459][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:32.460][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:32.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.463][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:32.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:32.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:32.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:32.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.472][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:32.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:32.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.477][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:32.478][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:32.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.479][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:32.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:32.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:32.540][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-08-29 14:07:32.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:32.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:32.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:32.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:32.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:32.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:32.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:32.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:32.565][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-08-29 14:07:32.566][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:32.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-08-29 14:07:32.571][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:32.572][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:32.573][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:32.574][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:32.576][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:32.578][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:32.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:32.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:32.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:32.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:32.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:32.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:32.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:32.595][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-08-29 14:07:32.598][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:32.599][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:32.601][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-08-29 14:07:32.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-08-29 14:07:32.793][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:32.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-08-29 14:07:32.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-08-29 14:07:32.804][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-08-29 14:07:32.805][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:32.806][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:32.807][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:32.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:32.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:32.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:32.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:32.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:32.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:32.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:32.824][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.827][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.843][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:32.844][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:32.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.846][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:32.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:32.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.851][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:32.851][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:32.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.853][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:32.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:32.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.858][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:32.859][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:32.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.860][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:32.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:32.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.867][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.869][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.870][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:32.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:32.876][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:32.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.878][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.879][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:32.880][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.881][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.883][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:32.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.886][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.887][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.889][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:32.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.896][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:32.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:32.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.899][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:32.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:32.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.906][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:32.907][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:32.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.908][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.909][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:32.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:32.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.913][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:32.914][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:32.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.916][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:32.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:32.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:32.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:32.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:32.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:32.974][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-08-29 14:07:32.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:32.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:32.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:32.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:32.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:32.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:32.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:32.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:32.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:32.998][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[2025-08-29 14:07:32.999][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-08-29 14:07:33.000][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:33.001][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-08-29 14:07:33.002][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:33.003][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:33.004][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:33.005][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:33.006][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:33.007][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:33.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:33.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:33.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:33.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:33.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:33.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:33.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:33.024][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-08-29 14:07:33.027][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:33.029][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:33.031][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-08-29 14:07:33.122][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-08-29 14:07:33.204][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:33.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-08-29 14:07:33.212][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-08-29 14:07:33.215][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-08-29 14:07:33.216][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:33.217][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:33.229][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:33.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:33.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:33.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:33.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:33.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:33.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:33.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:33.247][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.248][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.250][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.255][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:33.256][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:33.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.257][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.259][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:33.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:33.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.262][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:33.263][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:33.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.265][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:33.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:33.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.272][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:33.274][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:33.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.276][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:33.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:33.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.283][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.284][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.287][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.293][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:33.295][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:33.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.300][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.302][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:33.303][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.304][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:33.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.309][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.311][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.314][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.319][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:33.320][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:33.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.322][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:33.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:33.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.327][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:33.328][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:33.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.329][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:33.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:33.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.337][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:33.338][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:33.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.350][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.352][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:33.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:33.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:33.390][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-08-29 14:07:33.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:33.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:33.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:33.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:33.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:33.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:33.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:33.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:33.420][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-08-29 14:07:33.421][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:33.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-08-29 14:07:33.423][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:33.425][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:33.427][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:33.428][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:33.430][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:33.431][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:33.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:33.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:33.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:33.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:33.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:33.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:33.444][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.DEBUG[2025-08-29 14:07:33.445][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-08-29 14:07:33.456][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:33.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:33.459][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-08-29 14:07:33.544][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-08-29 14:07:33.621][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:33.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-08-29 14:07:33.630][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-08-29 14:07:33.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-08-29 14:07:33.636][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:33.638][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:33.640][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:33.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:33.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:33.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:33.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:33.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:33.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:33.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:33.658][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.661][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.666][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:33.667][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:33.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.668][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.670][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:33.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:33.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.673][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:33.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:33.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.676][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:33.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:33.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.685][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:33.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:33.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.690][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:33.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:33.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.695][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.696][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.698][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:33.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.702][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:33.706][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:33.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.708][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.709][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:33.712][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.714][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.717][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:33.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.722][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.723][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.725][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:33.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.730][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:33.741][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:33.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.744][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:33.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:33.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.749][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:33.750][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:33.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.754][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.756][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:33.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:33.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.760][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:33.761][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:33.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.763][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.764][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:33.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:33.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:33.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:33.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:33.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:33.812][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-08-29 14:07:33.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:33.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:33.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:33.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:33.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:33.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:33.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:33.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:33.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:33.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:33.837][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[2025-08-29 14:07:33.838][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-08-29 14:07:33.839][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:33.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-08-29 14:07:33.844][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:33.855][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:33.857][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:33.858][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:33.860][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:33.863][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:33.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:33.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:33.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:33.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:33.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:33.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:33.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:33.881][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-08-29 14:07:33.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:33.885][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:33.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-08-29 14:07:33.973][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-08-29 14:07:34.054][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:34.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-08-29 14:07:34.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-08-29 14:07:34.063][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-08-29 14:07:34.065][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:34.066][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:34.067][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:34.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:34.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:34.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:34.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:34.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:34.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:34.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:34.085][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.095][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:34.097][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:34.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.100][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.101][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:34.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:34.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.105][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:34.106][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:34.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.107][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.108][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:34.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:34.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:34.113][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:34.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.116][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:34.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:34.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.124][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.127][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.132][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:34.133][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:34.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.145][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.148][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:34.149][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.151][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.153][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:34.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.159][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.167][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:34.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:34.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.171][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:34.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:34.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.178][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:34.180][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:34.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.182][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:34.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:34.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:34.188][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:34.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.189][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.191][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:34.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:34.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:34.234][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-08-29 14:07:34.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:34.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:34.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:34.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:34.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:34.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:34.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:34.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:34.270][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-08-29 14:07:34.272][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:34.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-08-29 14:07:34.276][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:34.277][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:34.278][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:34.279][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:34.280][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:34.280][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:34.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:34.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:34.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:34.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:34.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:34.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:34.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:34.295][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-08-29 14:07:34.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:34.301][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:34.303][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-08-29 14:07:34.387][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-08-29 14:07:34.468][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:34.471][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-08-29 14:07:34.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-08-29 14:07:34.479][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-08-29 14:07:34.481][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:34.484][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:34.485][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:34.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:34.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:34.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:34.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:34.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:34.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:34.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:34.508][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.509][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.520][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:34.522][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:34.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.523][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.525][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:34.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:34.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.528][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:34.529][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:34.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.531][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:34.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:34.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.549][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:34.551][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:34.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.553][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:34.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.561][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.562][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.564][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.569][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:34.570][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:34.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.572][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.573][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:34.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.576][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.577][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:34.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.585][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.586][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.587][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:34.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.592][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:34.593][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:34.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.595][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:34.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:34.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.603][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:34.604][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:34.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.605][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.607][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:34.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:34.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:34.611][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:34.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.612][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.614][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:34.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:34.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:34.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:34.673][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-08-29 14:07:34.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:34.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:34.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:34.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:34.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:34.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:34.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:34.701][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[2025-08-29 14:07:34.702][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-08-29 14:07:34.703][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:34.704][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-08-29 14:07:34.705][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:34.706][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:34.707][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:34.708][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:34.709][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:34.710][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:34.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:34.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:34.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:34.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:34.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:34.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:34.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:34.727][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-08-29 14:07:34.730][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:34.731][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:34.733][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-08-29 14:07:34.817][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-08-29 14:07:34.895][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:34.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-08-29 14:07:34.902][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-08-29 14:07:34.905][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-08-29 14:07:34.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:34.908][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:34.909][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:34.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:34.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:34.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:34.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:34.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:34.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:34.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:34.926][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.928][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.929][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:34.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:34.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.951][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:34.952][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:34.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.954][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.955][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:34.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:34.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.962][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:34.963][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:34.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.965][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.966][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:34.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:34.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.970][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:34.971][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:34.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.973][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:34.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:34.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.980][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:34.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.989][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:34.989][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:34.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.991][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.992][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:34.993][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.995][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.996][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:34.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:34.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:34.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:34.999][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:35.000][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:35.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.002][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:35.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:35.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.012][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:35.013][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:35.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.015][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:35.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:35.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.020][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:35.021][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:35.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.023][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.024][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:35.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:35.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.031][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:35.033][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:35.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.035][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:35.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:35.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:35.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:35.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:35.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:35.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:35.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:35.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:35.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:35.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:35.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:35.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:35.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:35.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:35.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:35.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:35.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:35.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:35.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:35.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.093][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-08-29 14:07:35.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.128][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:35.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:35.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 14:07:35.137][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:35.139][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 14:07:35.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.158][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[2025-08-29 14:07:35.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.429][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[2025-08-29 14:07:35.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.499][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.TRACE[2025-08-29 14:07:35.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.559][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.TRACE[2025-08-29 14:07:35.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.610][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[2025-08-29 14:07:35.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.696][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[2025-08-29 14:07:35.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.725][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[2025-08-29 14:07:35.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.789][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.TRACE[2025-08-29 14:07:35.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.849][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.TRACE[2025-08-29 14:07:35.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:35.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:35.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:35.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:35.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:35.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:35.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:35.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:35.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:35.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:35.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:35.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:36.049][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[2025-08-29 14:07:36.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:36.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:36.056][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 14:07:36.137][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 14:07:36.212][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:36.215][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-08-29 14:07:36.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-08-29 14:07:36.226][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:36.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:36.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:36.234][private$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[2025-08-29 14:07:36.313][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[2025-08-29 14:07:36.394][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:36.398][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-08-29 14:07:36.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-08-29 14:07:36.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:36.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:36.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:36.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:36.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:36.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:36.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:36.420][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-08-29 14:07:36.421][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:36.423][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-08-29 14:07:36.425][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:36.426][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:36.427][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:36.428][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:36.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:36.431][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:36.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:36.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:36.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:36.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:36.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:36.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:36.446][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[2025-08-29 14:07:36.447][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-08-29 14:07:36.450][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:36.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:36.453][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-08-29 14:07:36.544][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-08-29 14:07:36.622][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:36.625][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-08-29 14:07:36.630][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-08-29 14:07:36.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-08-29 14:07:36.634][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:36.635][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:36.636][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:36.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:36.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:36.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:36.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:36.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:36.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:36.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:36.654][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.655][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.657][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.662][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:36.664][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:36.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.665][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.667][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:36.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:36.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.671][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:36.672][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:36.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.674][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:36.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:36.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.683][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:36.684][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:36.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.686][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:36.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:36.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.691][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:36.692][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:36.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.694][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:36.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:36.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.702][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:36.703][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:36.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.705][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.707][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:36.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:36.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.711][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:36.712][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:36.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.714][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.715][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:36.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:36.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.719][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.721][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.724][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.730][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:36.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:36.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.733][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:36.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:36.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.739][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:36.740][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:36.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.743][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.745][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:36.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:36.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.750][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:36.751][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:36.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.752][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.754][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:36.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:36.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:36.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:36.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:36.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:36.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:36.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:36.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:36.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:36.819][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-08-29 14:07:36.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:36.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:36.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:36.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:36.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:36.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:36.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:36.848][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.TRACE[2025-08-29 14:07:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:36.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:36.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:36.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:36.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:36.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:36.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:36.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:36.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:36.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:36.876][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[2025-08-29 14:07:36.877][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-08-29 14:07:36.878][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:36.879][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-08-29 14:07:36.881][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:36.882][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:36.882][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:36.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:36.884][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:36.885][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:36.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:36.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:36.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:36.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:36.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:36.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:36.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:36.906][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-08-29 14:07:36.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:36.910][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-08-29 14:07:36.912][rule$waitAsNeeded] Wait 0.143663 second(s).
biodb.TRACE[2025-08-29 14:07:37.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-08-29 14:07:37.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-08-29 14:07:37.369][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:37.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-08-29 14:07:37.376][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-08-29 14:07:37.379][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-08-29 14:07:37.381][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:37.382][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:37.383][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:37.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.398][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[2025-08-29 14:07:37.400][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.401][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.404][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.411][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:37.412][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:37.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.413][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.415][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:37.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:37.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.421][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:37.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:37.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.424][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:37.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:37.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.430][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:37.431][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:37.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.433][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.434][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:37.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:37.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.438][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:37.438][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:37.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.440][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:37.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:37.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.447][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:37.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:37.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.450][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.452][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:37.452][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:37.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.454][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.455][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:37.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:37.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.469][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.470][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.471][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.477][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:37.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:37.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.483][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:37.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:37.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.489][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:37.490][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:37.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.492][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.493][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:37.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:37.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.498][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:37.499][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:37.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.502][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.505][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:37.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:37.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:37.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:37.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:37.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:37.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:37.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:37.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:37.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.549][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-08-29 14:07:37.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.581][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:37.585][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:37.587][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 14:07:37.589][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:37.591][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 14:07:37.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:37.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:37.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:37.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:37.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:37.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:37.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:37.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:37.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:37.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:37.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:37.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.190][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:38.194][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:38.195][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 14:07:38.199][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:38.200][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 14:07:38.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:38.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.773][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:38.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:38.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:38.785][biodb::testThat]
biodb.INFO [2025-08-29 14:07:38.787][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-29 14:07:38.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:38.788][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:38.791][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 14:07:38.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 14:07:38.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:38.833][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:38.837][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:38.838][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 14:07:38.839][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:38.840][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 14:07:38.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.868][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:38.872][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:38.874][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 14:07:38.876][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:38.877][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 14:07:38.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:38.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:38.938][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 14:07:38.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:38.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:38.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:38.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:38.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:38.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:38.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:38.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.960][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:38.961][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:38.962][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:38.963][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:38.963][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:38.964][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.965][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.967][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.970][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.971][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:38.972][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:38.973][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.974][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.975][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.976][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:38.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:38.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:38.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.001][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 14:07:39.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.022][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.027][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:39.028][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:39.030][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:39.031][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.032][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.033][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.035][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.036][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.039][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.040][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.041][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.042][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.043][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.045][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.046][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:39.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.063][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 14:07:39.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.088][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.090][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:39.091][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:39.091][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:39.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.093][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.096][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.097][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.100][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.101][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.102][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.103][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.105][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.106][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:39.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.120][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 14:07:39.121][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 14:07:39.122][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 14:07:39.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:39.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:39.231][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:39.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:39.236][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:39.238][private$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[2025-08-29 14:07:39.321][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[2025-08-29 14:07:39.399][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:39.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-08-29 14:07:39.407][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-08-29 14:07:39.411][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[2025-08-29 14:07:39.415][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:39.416][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:39.417][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 14:07:39.502][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 14:07:39.580][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:39.583][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-08-29 14:07:39.588][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-08-29 14:07:39.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:39.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:39.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:39.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:39.720][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 14:07:39.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.771][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:39.772][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:39.772][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:39.773][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.777][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.777][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.780][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.781][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.784][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.785][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.787][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.788][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.789][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:39.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.801][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 14:07:39.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.864][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:39.865][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:39.866][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:39.867][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.868][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.869][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.871][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.872][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.873][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.875][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.876][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.888][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.890][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.891][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.894][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.895][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:39.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.906][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 14:07:39.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:39.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:39.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:39.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:39.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:39.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:39.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:39.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.931][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.931][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:39.932][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:39.933][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:39.935][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.936][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.939][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.941][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.943][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.944][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.947][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.949][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.950][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:39.951][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.953][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.955][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.955][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:39.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:39.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:39.974][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 14:07:39.975][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 14:07:39.977][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 14:07:39.987][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:39.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:39.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:39.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:39.999][biodb::testThat]
biodb.INFO [2025-08-29 14:07:40.000][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-29 14:07:40.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:40.002][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:40.005][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 14:07:40.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 14:07:40.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:40.059][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:40.063][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:40.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 14:07:40.065][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:40.067][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 14:07:40.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.096][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:40.099][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:40.101][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 14:07:40.102][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:40.104][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 14:07:40.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.165][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 14:07:40.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.188][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.189][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.191][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.193][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.202][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.203][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.205][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.207][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.208][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.209][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.210][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.211][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.213][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.215][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.229][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 14:07:40.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.244][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[2025-08-29 14:07:40.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.253][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.253][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.254][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.255][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.256][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.257][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.258][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.259][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.260][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.261][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.263][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.264][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.264][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.265][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.266][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.268][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.269][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.286][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 14:07:40.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.310][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.311][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.312][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.312][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.313][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.314][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.315][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.317][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.317][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.319][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.323][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.325][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.326][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.328][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.329][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.330][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.342][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 14:07:40.343][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 14:07:40.344][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 14:07:40.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:40.391][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:40.396][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:40.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-29 14:07:40.399][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:40.400][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-29 14:07:40.405][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:40.409][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:40.412][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-29 14:07:40.414][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:40.417][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-29 14:07:40.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:40.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.508][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 14:07:40.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.530][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.531][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.533][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.534][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.535][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.537][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.539][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.539][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.540][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.544][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.545][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.546][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.547][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.548][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.551][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.552][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.568][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 14:07:40.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.588][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.588][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.589][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.590][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.591][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.592][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.597][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.598][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.599][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.601][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.602][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.603][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.604][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.605][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.606][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.620][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 14:07:40.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.644][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.644][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.645][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.646][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.647][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.648][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.649][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.652][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.653][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.655][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.657][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.658][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.659][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.660][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.662][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.663][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.674][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 14:07:40.675][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 14:07:40.678][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 14:07:40.688][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:40.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:40.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:40.697][biodb::testThat]
biodb.INFO [2025-08-29 14:07:40.698][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-29 14:07:40.699][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:40.700][biodb::testThat]
biodb.TRACE[2025-08-29 14:07:40.703][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 14:07:40.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 14:07:40.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:40.745][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:40.748][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:40.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 14:07:40.751][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:40.753][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 14:07:40.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.785][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:40.790][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:40.792][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 14:07:40.793][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:40.795][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 14:07:40.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:40.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:40.849][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 14:07:40.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.872][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.873][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.874][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.881][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.883][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.886][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.888][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.890][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.891][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.893][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.894][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.895][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.896][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.897][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.898][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.899][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.911][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 14:07:40.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.925][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.TRACE[2025-08-29 14:07:40.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.934][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.935][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.935][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.936][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.937][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.938][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.939][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.941][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.942][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.943][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.944][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.945][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.946][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.947][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.948][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.951][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.952][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:40.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 14:07:40.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:40.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:40.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:40.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:40.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:40.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:40.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:40.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.987][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.988][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:40.989][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:40.990][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:40.991][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:40.992][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.993][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.995][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.995][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.996][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:40.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:40.998][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:40.999][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.000][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.001][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.002][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.003][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.005][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:41.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.020][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 14:07:41.021][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 14:07:41.022][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 14:07:41.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:41.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:41.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:41.084][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:41.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-29 14:07:41.086][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:41.088][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-29 14:07:41.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:41.095][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:41.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-29 14:07:41.097][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:41.099][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-29 14:07:41.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:41.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:41.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:41.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:41.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:41.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:41.180][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 14:07:41.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:41.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.202][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.203][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:41.205][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:41.206][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:41.207][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.208][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.216][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.218][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.219][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.221][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.222][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.228][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.229][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:41.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.242][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 14:07:41.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:41.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.266][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.267][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:41.268][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:41.268][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:41.269][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.270][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.271][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.286][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.288][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.293][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.305][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.306][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.307][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.307][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.308][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.310][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.311][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:41.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.325][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 14:07:41.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:41.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.349][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 14:07:41.349][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 14:07:41.350][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 14:07:41.351][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.352][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.354][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.355][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.356][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.358][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.360][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.361][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 14:07:41.362][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.363][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.365][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.365][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 14:07:41.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.380][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 14:07:41.381][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 14:07:41.382][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 14:07:41.405][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:41.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 14:07:41.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:41.415][biodb::testThat]
biodb.INFO [2025-08-29 14:07:41.417][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-08-29 14:07:41.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:41.419][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:41.421][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-08-29 14:07:41.422][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:41.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-08-29 14:07:41.425][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 14:07:41.426][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 14:07:41.427][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:41.428][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:41.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:41.430][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:41.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:41.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-08-29 14:07:41.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:41.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:41.449][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-08-29 14:07:41.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-08-29 14:07:41.629][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:41.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-08-29 14:07:41.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-08-29 14:07:41.640][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-08-29 14:07:41.642][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:41.644][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:41.646][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:41.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:41.663][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.664][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.666][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.671][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:41.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:41.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.673][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.675][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:41.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:41.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.677][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.679][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:41.680][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:41.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.682][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.683][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:41.684][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:41.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.690][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.691][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:41.692][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:41.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.694][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.696][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:41.697][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:41.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.699][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.700][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.702][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:41.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.705][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.707][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:41.708][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:41.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.710][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.711][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:41.712][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:41.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.714][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.715][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:41.716][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:41.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.717][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:41.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:41.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:41.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:41.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:41.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:41.764][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-08-29 14:07:41.765][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-08-29 14:07:41.774][biodb::testThat]
biodb.INFO [2025-08-29 14:07:41.775][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-08-29 14:07:41.776][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:41.777][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:41.788][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-08-29 14:07:41.790][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-08-29 14:07:41.792][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-08-29 14:07:41.796][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-08-29 14:07:41.798][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2025-08-29 14:07:41.800][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2025-08-29 14:07:41.801][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:41.802][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:41.803][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 14:07:41.804][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 14:07:41.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:41.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:41.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:41.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:41.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:41.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:41.821][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-08-29 14:07:41.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:41.825][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:41.826][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-08-29 14:07:41.903][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-08-29 14:07:41.985][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:41.990][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-08-29 14:07:41.995][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-08-29 14:07:41.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:41.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:42.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:42.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:42.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:42.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:42.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:42.013][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-08-29 14:07:42.016][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:42.017][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:42.018][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-08-29 14:07:42.110][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-08-29 14:07:42.192][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:42.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-08-29 14:07:42.199][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-08-29 14:07:42.202][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-08-29 14:07:42.204][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 14:07:42.205][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-08-29 14:07:42.207][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:42.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:42.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:42.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:42.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:42.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:42.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:42.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:42.241][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.243][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.245][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.249][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:42.250][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:42.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.252][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.253][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:42.254][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:42.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.255][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.257][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:42.258][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:42.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.259][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.260][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.261][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.264][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.266][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.268][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.270][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.271][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:42.272][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:42.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.274][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.275][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.277][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.280][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:42.281][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:42.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.283][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.285][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:42.286][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:42.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.289][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.290][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:42.291][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:42.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.293][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:42.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:42.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:42.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:42.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:42.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:42.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:42.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:42.336][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.338][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.339][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.344][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:42.345][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:42.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.347][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.348][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:42.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:42.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.352][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:42.353][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:42.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.355][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:42.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.360][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:42.361][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:42.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.362][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:42.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:42.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.369][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.370][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.372][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.377][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.378][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.380][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.384][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:42.385][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:42.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.388][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.396][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.397][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.398][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.403][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:42.404][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:42.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.405][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.410][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:42.411][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:42.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.414][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.415][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:42.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:42.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.420][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:42.421][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:42.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.422][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:42.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:42.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:42.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:42.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:42.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:42.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:42.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:42.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 14:07:42.480][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.481][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.483][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.490][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:42.491][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:42.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.492][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.494][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:42.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:42.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.497][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:42.498][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:42.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.500][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:42.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:42.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.504][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:42.505][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:42.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.507][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:42.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:42.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.514][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.515][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.517][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:42.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.522][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.524][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.526][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.531][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:42.532][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:42.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.535][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.537][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:42.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.541][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.542][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.544][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:42.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.550][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:42.551][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:42.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.552][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:42.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:42.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.557][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:42.558][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:42.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.560][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.561][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:42.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:42.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.564][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:42.565][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:42.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.567][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:42.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:42.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:42.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:42.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:42.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:42.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:42.648][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-08-29 14:07:42.649][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-08-29 14:07:42.650][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-08-29 14:07:42.666][biodb::testThat]
biodb.INFO [2025-08-29 14:07:42.668][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-08-29 14:07:42.669][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:42.669][biodb::testThat]
biodb.INFO [2025-08-29 14:07:42.698][biodb::testThat]
biodb.INFO [2025-08-29 14:07:42.699][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-08-29 14:07:42.700][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:42.701][biodb::testThat]
biodb.INFO [2025-08-29 14:07:42.710][biodb::testThat]
biodb.INFO [2025-08-29 14:07:42.713][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-08-29 14:07:42.714][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:42.715][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:42.718][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[2025-08-29 14:07:42.722][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:42.723][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:42.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-08-29 14:07:42.869][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-08-29 14:07:42.989][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:42.993][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-08-29 14:07:42.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-08-29 14:07:43.012][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:43.014][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:43.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:43.018][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:43.019][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:43.020][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:43.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:43.022][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 14:07:43.023][biodb::testThat]
biodb.INFO [2025-08-29 14:07:43.024][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-08-29 14:07:43.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:43.026][biodb::testThat]
biodb.ERROR[2025-08-29 14:07:43.042][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-08-29 14:07:43.060][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-08-29 14:07:43.076][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 14:07:43.078][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 14:07:43.079][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 14:07:43.080][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 14:07:43.081][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.082][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.084][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 14:07:43.095][biodb::testContext]
biodb.INFO [2025-08-29 14:07:43.097][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:43.098][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-08-29 14:07:43.100][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:43.101][biodb::testContext]
biodb.INFO [2025-08-29 14:07:43.104][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:43.106][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:43.111][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:43.112][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 14:07:43.113][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 14:07:43.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.116][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 14:07:43.117][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 14:07:43.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.121][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 14:07:43.123][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 14:07:43.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.127][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 14:07:43.128][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 14:07:43.129][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 14:07:43.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.135][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 14:07:43.136][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 14:07:43.138][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 14:07:43.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.142][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 14:07:43.142][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 14:07:43.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.146][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 14:07:43.148][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 14:07:43.149][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 14:07:43.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.153][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 14:07:43.154][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 14:07:43.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.157][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 14:07:43.158][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 14:07:43.159][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 14:07:43.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.162][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:43.163][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 14:07:43.163][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 14:07:43.164][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 14:07:43.165][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 14:07:43.166][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 14:07:43.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.171][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 14:07:43.172][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 14:07:43.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.175][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 14:07:43.176][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 14:07:43.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.179][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 14:07:43.180][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 14:07:43.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.183][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 14:07:43.184][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 14:07:43.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.189][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 14:07:43.190][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 14:07:43.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.194][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:43.195][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 14:07:43.219][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 14:07:43.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.225][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 14:07:43.226][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 14:07:43.227][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 14:07:43.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.230][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 14:07:43.232][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.233][self$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[2025-08-29 14:07:43.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.234][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:43.235][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.236][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.237][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.238][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.239][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:43.240][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:43.242][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.243][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 14:07:43.244][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:43.245][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.246][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.247][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:43.247][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:43.247][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:43.247][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:43.247][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:43.248][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:43.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:43.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.256][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.257][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:43.258][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:43.259][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.260][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.261][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 14:07:43.263][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.264][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:43.265][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.266][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:43.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.268][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.268][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.269][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.270][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:43.271][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:43.272][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.272][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 14:07:43.273][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:43.274][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.275][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.276][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:43.276][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:43.276][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:43.276][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:43.276][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:43.277][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:43.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.291][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:43.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.294][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.295][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.296][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:43.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:43.299][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.300][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.302][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 14:07:43.304][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.305][self$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[2025-08-29 14:07:43.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:43.307][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.309][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.310][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.311][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:43.312][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:43.313][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.314][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 14:07:43.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:43.316][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.316][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.318][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.319][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:43.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:43.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.325][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.326][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.327][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:43.328][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:43.328][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.329][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.330][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 14:07:43.332][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.333][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:43.334][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:43.336][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.336][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.337][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.338][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.339][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:43.340][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:43.341][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.341][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 14:07:43.342][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:43.344][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.346][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.347][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:43.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.352][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:43.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.355][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.356][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:43.357][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:43.358][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.358][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:43.360][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:43.361][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.362][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[2025-08-29 14:07:43.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.366][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[2025-08-29 14:07:43.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.388][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[2025-08-29 14:07:43.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.394][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[2025-08-29 14:07:43.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.398][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[2025-08-29 14:07:43.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.406][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[2025-08-29 14:07:43.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.409][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[2025-08-29 14:07:43.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.413][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[2025-08-29 14:07:43.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.446][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 14:07:43.447][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 14:07:43.449][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 14:07:43.450][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 14:07:43.451][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:43.454][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 14:07:43.456][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:43.458][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:43.460][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 14:07:43.462][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 14:07:43.463][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:43.464][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 14:07:43.466][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:43.468][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:43.470][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 14:07:43.472][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 14:07:43.473][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 14:07:43.474][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 14:07:43.476][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:43.477][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 14:07:43.478][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 14:07:43.479][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 14:07:43.480][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 14:07:43.482][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 14:07:43.483][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 14:07:43.484][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 14:07:43.485][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 14:07:43.486][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 14:07:43.488][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 14:07:43.490][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 14:07:43.494][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 14:07:43.496][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 14:07:43.498][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 14:07:43.500][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 14:07:43.501][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 14:07:43.502][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 14:07:43.504][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 14:07:43.506][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 14:07:43.509][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 14:07:43.511][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 14:07:43.513][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 14:07:43.515][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 14:07:43.517][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 14:07:43.518][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 14:07:43.519][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 14:07:43.521][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 14:07:43.522][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 14:07:43.523][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 14:07:43.524][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 14:07:43.525][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 14:07:43.527][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 14:07:43.528][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 14:07:43.529][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 14:07:43.530][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 14:07:43.533][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 14:07:43.535][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 14:07:43.536][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 14:07:43.539][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 14:07:43.541][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 14:07:43.542][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 14:07:43.543][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 14:07:43.544][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 14:07:43.545][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 14:07:43.547][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 14:07:43.548][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 14:07:43.549][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 14:07:43.551][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:43.553][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:43.555][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 14:07:43.557][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 14:07:43.558][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 14:07:43.559][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 14:07:43.561][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 14:07:43.562][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 14:07:43.563][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 14:07:43.564][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 14:07:43.565][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 14:07:43.568][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 14:07:43.571][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 14:07:43.573][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 14:07:43.574][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 14:07:43.575][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 14:07:43.577][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 14:07:43.578][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 14:07:43.580][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:43.581][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:43.581][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.583][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:43.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.714][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:43.716][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 14:07:43.718][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.719][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.720][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.721][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:43.721][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.723][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.724][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 14:07:43.725][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 14:07:43.726][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:43.726][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.729][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 14:07:43.730][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 14:07:43.731][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 14:07:43.733][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:43.733][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:43.733][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:43.733][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:43.734][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 14:07:43.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.737][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:43.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:43.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:43.741][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:43.742][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:43.742][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 14:07:43.743][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:43.744][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:43.745][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:43.746][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 14:07:43.746][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 14:07:43.747][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:43.749][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:43.750][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 14:07:43.753][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:43.755][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:43.757][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:43.760][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 14:07:43.761][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 14:07:43.762][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 14:07:43.764][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 14:07:43.765][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:43.766][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:43.767][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 14:07:43.768][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 14:07:43.769][biodb::testThat]
biodb.INFO [2025-08-29 14:07:43.770][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-08-29 14:07:43.772][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:43.775][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:43.780][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 14:07:43.784][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:43.786][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 14:07:43.787][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:43.788][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 14:07:43.792][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:43.797][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:43.800][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 14:07:43.801][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:43.803][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 14:07:43.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.822][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:43.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:43.828][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 14:07:43.829][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:43.831][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 14:07:43.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.878][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[2025-08-29 14:07:43.884][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:43.887][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:43.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 14:07:43.890][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:43.891][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 14:07:43.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.907][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:43.912][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:43.914][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 14:07:43.915][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:43.917][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 14:07:43.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.931][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[2025-08-29 14:07:43.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.948][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:43.953][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:43.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 14:07:43.957][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:43.958][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 14:07:43.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.972][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:43.977][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:43.978][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 14:07:43.982][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:43.984][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 14:07:43.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:43.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:43.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:43.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:43.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:43.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:43.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:43.998][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:44.002][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:44.004][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-08-29 14:07:44.006][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:44.008][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-08-29 14:07:44.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:44.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 14:07:44.028][biodb::testThat]
biodb.INFO [2025-08-29 14:07:44.029][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-08-29 14:07:44.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:44.031][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:44.034][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:44.038][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:44.039][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:44.042][private$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[2025-08-29 14:07:44.149][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[2025-08-29 14:07:44.224][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:44.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-08-29 14:07:44.232][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-08-29 14:07:44.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:44.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.252][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[2025-08-29 14:07:44.256][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 14:07:44.257][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 14:07:44.258][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-29 14:07:44.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-29 14:07:44.413][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 14:07:44.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-08-29 14:07:44.438][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-08-29 14:07:44.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:44.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 14:07:44.457][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 14:07:44.458][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 14:07:44.459][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 14:07:44.460][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 14:07:44.461][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.462][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.464][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 14:07:44.469][biodb::testContext]
biodb.INFO [2025-08-29 14:07:44.470][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:44.471][biodb::testContext] Test context - Test web services
biodb.INFO [2025-08-29 14:07:44.472][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:44.473][biodb::testContext]
biodb.INFO [2025-08-29 14:07:44.475][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:44.477][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:44.482][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:44.483][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 14:07:44.484][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 14:07:44.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.487][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 14:07:44.488][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 14:07:44.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.491][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 14:07:44.492][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 14:07:44.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.495][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 14:07:44.496][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 14:07:44.496][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 14:07:44.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.499][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 14:07:44.501][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 14:07:44.502][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 14:07:44.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.506][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 14:07:44.507][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 14:07:44.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.512][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 14:07:44.513][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 14:07:44.514][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 14:07:44.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.517][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 14:07:44.518][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 14:07:44.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.521][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 14:07:44.522][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 14:07:44.523][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 14:07:44.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.526][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:44.527][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 14:07:44.528][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 14:07:44.529][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 14:07:44.530][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 14:07:44.531][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 14:07:44.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.534][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 14:07:44.535][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 14:07:44.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.538][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 14:07:44.539][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 14:07:44.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.542][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 14:07:44.543][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 14:07:44.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.547][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 14:07:44.548][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 14:07:44.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.551][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 14:07:44.552][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 14:07:44.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.555][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:44.556][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 14:07:44.576][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 14:07:44.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.582][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 14:07:44.583][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 14:07:44.584][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 14:07:44.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.587][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 14:07:44.589][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.589][self$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[2025-08-29 14:07:44.590][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.591][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:44.592][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.594][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.595][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.599][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.600][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:44.601][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:44.603][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.604][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 14:07:44.605][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:44.606][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.606][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.607][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:44.607][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:44.607][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:44.607][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:44.607][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:44.608][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:44.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:44.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.614][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:44.615][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:44.616][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.617][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.618][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 14:07:44.621][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.622][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:44.623][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.624][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:44.625][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.626][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.626][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.627][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.628][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:44.629][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:44.630][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.631][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 14:07:44.632][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:44.633][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.634][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.635][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:44.635][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:44.635][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:44.635][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:44.635][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:44.636][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:44.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.639][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:44.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.641][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.642][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.642][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:44.643][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:44.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.646][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.647][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 14:07:44.649][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.650][self$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[2025-08-29 14:07:44.651][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.652][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:44.653][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.653][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.654][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.655][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.656][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:44.657][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:44.658][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.659][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 14:07:44.660][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:44.660][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.661][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.662][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.663][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:44.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.665][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:44.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.667][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.668][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:44.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:44.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.671][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.672][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 14:07:44.674][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.675][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:44.676][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.677][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:44.678][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.679][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.682][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:44.683][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:44.683][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.684][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 14:07:44.685][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:44.686][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.687][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:44.688][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.688][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:44.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:44.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:44.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:44.693][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:44.694][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.695][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:44.698][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:44.699][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:44.700][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:44.702][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:44.703][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.746][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[2025-08-29 14:07:44.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.753][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[2025-08-29 14:07:44.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.764][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.DEBUG[2025-08-29 14:07:44.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.769][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 14:07:44.770][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 14:07:44.772][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 14:07:44.773][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 14:07:44.782][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:44.783][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 14:07:44.784][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:44.786][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:44.787][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 14:07:44.788][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 14:07:44.789][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:44.790][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 14:07:44.791][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:44.792][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:44.794][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 14:07:44.795][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 14:07:44.796][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 14:07:44.797][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 14:07:44.798][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:44.799][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 14:07:44.801][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 14:07:44.802][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 14:07:44.803][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 14:07:44.804][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 14:07:44.805][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 14:07:44.806][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 14:07:44.808][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 14:07:44.810][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 14:07:44.811][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 14:07:44.812][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 14:07:44.813][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 14:07:44.814][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 14:07:44.815][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 14:07:44.817][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 14:07:44.818][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 14:07:44.819][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 14:07:44.820][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 14:07:44.821][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 14:07:44.822][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 14:07:44.824][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 14:07:44.826][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 14:07:44.827][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 14:07:44.829][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 14:07:44.830][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 14:07:44.831][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 14:07:44.832][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 14:07:44.834][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 14:07:44.836][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 14:07:44.837][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 14:07:44.839][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 14:07:44.841][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 14:07:44.842][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 14:07:44.844][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 14:07:44.846][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 14:07:44.847][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 14:07:44.849][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 14:07:44.851][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 14:07:44.852][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 14:07:44.854][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 14:07:44.855][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 14:07:44.857][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 14:07:44.859][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 14:07:44.861][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 14:07:44.862][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 14:07:44.864][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 14:07:44.866][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 14:07:44.867][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:44.869][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:44.870][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 14:07:44.872][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 14:07:44.874][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 14:07:44.876][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 14:07:44.877][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 14:07:44.878][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 14:07:44.879][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 14:07:44.881][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 14:07:44.882][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 14:07:44.883][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 14:07:44.885][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 14:07:44.886][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 14:07:44.888][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 14:07:44.889][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 14:07:44.891][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 14:07:44.893][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 14:07:44.895][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:44.896][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:44.897][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.899][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.900][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[2025-08-29 14:07:44.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.915][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[2025-08-29 14:07:44.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.920][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[2025-08-29 14:07:44.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.925][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[2025-08-29 14:07:44.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.937][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[2025-08-29 14:07:44.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.957][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[2025-08-29 14:07:44.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:44.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:44.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:44.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:44.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:44.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:44.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:44.996][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[2025-08-29 14:07:44.999][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:45.001][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 14:07:45.003][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.004][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.005][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.006][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:45.007][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.008][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.009][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.009][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 14:07:45.010][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 14:07:45.011][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:45.012][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.013][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 14:07:45.014][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 14:07:45.015][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 14:07:45.016][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.016][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:45.016][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:45.016][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:45.017][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 14:07:45.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:45.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.024][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:45.024][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 14:07:45.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:45.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:45.027][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.028][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 14:07:45.028][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 14:07:45.029][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:45.031][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:45.033][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 14:07:45.035][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:45.037][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:45.040][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:45.044][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 14:07:45.045][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 14:07:45.047][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 14:07:45.048][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 14:07:45.050][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:45.050][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:45.052][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 14:07:45.053][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 14:07:45.054][biodb::testThat]
biodb.INFO [2025-08-29 14:07:45.055][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-08-29 14:07:45.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:45.057][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:45.061][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 14:07:45.065][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:45.067][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 14:07:45.068][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:45.070][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 14:07:45.075][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:45.079][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:45.081][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-08-29 14:07:45.083][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:45.085][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2025-08-29 14:07:45.094][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 14:07:45.096][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 14:07:45.097][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 14:07:45.098][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 14:07:45.099][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.100][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.102][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 14:07:45.108][biodb::testContext]
biodb.INFO [2025-08-29 14:07:45.109][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:45.110][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-08-29 14:07:45.111][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 14:07:45.112][biodb::testContext]
biodb.INFO [2025-08-29 14:07:45.114][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:45.116][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:45.121][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:45.122][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 14:07:45.123][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 14:07:45.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.137][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 14:07:45.138][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 14:07:45.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.141][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 14:07:45.142][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 14:07:45.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.144][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[2025-08-29 14:07:45.145][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 14:07:45.146][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 14:07:45.147][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 14:07:45.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.150][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 14:07:45.151][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 14:07:45.152][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 14:07:45.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.155][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 14:07:45.156][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 14:07:45.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.159][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 14:07:45.160][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 14:07:45.161][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 14:07:45.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.163][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 14:07:45.164][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 14:07:45.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.167][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 14:07:45.168][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 14:07:45.169][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 14:07:45.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.172][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:45.173][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 14:07:45.174][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 14:07:45.175][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 14:07:45.175][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 14:07:45.176][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 14:07:45.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.179][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 14:07:45.180][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 14:07:45.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.183][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 14:07:45.184][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 14:07:45.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.187][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 14:07:45.188][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 14:07:45.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.190][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 14:07:45.191][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 14:07:45.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.194][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 14:07:45.195][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 14:07:45.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.198][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 14:07:45.199][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 14:07:45.222][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 14:07:45.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.226][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 14:07:45.227][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 14:07:45.229][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 14:07:45.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.232][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 14:07:45.234][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.235][self$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[2025-08-29 14:07:45.236][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.237][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:45.237][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.238][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.239][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.240][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.241][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:45.242][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:45.243][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.244][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 14:07:45.244][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:45.245][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.246][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.247][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:45.247][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:45.247][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:45.247][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:45.247][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:45.248][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:45.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:45.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.253][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.254][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.255][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:45.255][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:45.256][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.257][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.258][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 14:07:45.260][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.261][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:45.262][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.262][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:45.263][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.264][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.265][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.267][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:45.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:45.268][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.269][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 14:07:45.270][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:45.271][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.272][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.272][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:45.272][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:45.272][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:45.272][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 14:07:45.272][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 14:07:45.273][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:45.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.276][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:45.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.278][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.279][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.280][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:45.280][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:45.281][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.282][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.283][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 14:07:45.285][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.286][self$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[2025-08-29 14:07:45.287][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:45.289][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.289][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.290][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.292][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 14:07:45.293][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:45.294][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.295][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 14:07:45.295][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:45.296][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.297][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.298][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.299][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:45.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:45.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.306][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.307][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.308][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:45.309][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:45.310][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.311][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.312][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 14:07:45.314][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.315][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 14:07:45.315][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.316][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:45.318][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.319][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.321][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.322][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.323][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 14:07:45.324][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:45.325][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.325][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 14:07:45.326][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:45.327][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.328][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.329][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.330][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 14:07:45.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:45.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.334][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.335][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.336][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:45.337][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:45.338][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.339][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 14:07:45.340][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:45.341][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.342][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[2025-08-29 14:07:45.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.372][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[2025-08-29 14:07:45.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.379][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.DEBUG[2025-08-29 14:07:45.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.388][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[2025-08-29 14:07:45.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.393][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[2025-08-29 14:07:45.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.404][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[2025-08-29 14:07:45.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.412][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 14:07:45.414][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 14:07:45.415][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 14:07:45.416][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 14:07:45.417][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:45.419][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 14:07:45.420][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:45.421][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:45.423][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 14:07:45.424][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 14:07:45.425][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:45.426][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 14:07:45.427][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 14:07:45.428][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 14:07:45.430][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 14:07:45.431][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 14:07:45.432][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 14:07:45.433][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 14:07:45.434][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:45.435][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 14:07:45.437][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 14:07:45.438][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 14:07:45.439][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 14:07:45.440][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 14:07:45.441][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 14:07:45.443][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 14:07:45.444][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 14:07:45.445][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 14:07:45.447][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 14:07:45.449][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 14:07:45.450][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 14:07:45.452][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 14:07:45.461][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 14:07:45.463][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 14:07:45.464][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 14:07:45.465][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 14:07:45.467][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 14:07:45.468][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 14:07:45.470][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 14:07:45.472][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 14:07:45.474][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 14:07:45.476][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 14:07:45.477][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 14:07:45.479][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 14:07:45.480][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 14:07:45.481][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 14:07:45.482][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 14:07:45.484][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 14:07:45.485][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 14:07:45.486][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 14:07:45.487][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 14:07:45.488][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 14:07:45.490][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 14:07:45.491][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 14:07:45.492][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 14:07:45.493][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 14:07:45.495][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 14:07:45.496][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 14:07:45.497][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 14:07:45.498][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 14:07:45.499][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 14:07:45.501][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 14:07:45.502][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 14:07:45.503][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 14:07:45.504][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 14:07:45.507][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 14:07:45.509][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:45.510][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:45.512][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 14:07:45.514][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 14:07:45.516][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 14:07:45.518][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 14:07:45.519][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 14:07:45.521][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 14:07:45.522][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 14:07:45.524][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 14:07:45.525][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 14:07:45.527][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 14:07:45.528][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 14:07:45.529][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 14:07:45.531][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 14:07:45.533][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 14:07:45.534][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 14:07:45.536][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 14:07:45.538][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 14:07:45.539][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 14:07:45.540][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.542][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.559][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[2025-08-29 14:07:45.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.581][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[2025-08-29 14:07:45.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.629][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[2025-08-29 14:07:45.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 14:07:45.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 14:07:45.651][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 14:07:45.652][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 14:07:45.656][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.657][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.659][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.660][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 14:07:45.660][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.661][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.662][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.663][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 14:07:45.664][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 14:07:45.665][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 14:07:45.667][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.669][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 14:07:45.671][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 14:07:45.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 14:07:45.673][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 14:07:45.674][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 14:07:45.674][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 14:07:45.674][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 14:07:45.675][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 14:07:45.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.677][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 14:07:45.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 14:07:45.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 14:07:45.680][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 14:07:45.680][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 14:07:45.680][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 14:07:45.681][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 14:07:45.682][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 14:07:45.683][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 14:07:45.684][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 14:07:45.684][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 14:07:45.685][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 14:07:45.687][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 14:07:45.688][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 14:07:45.690][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 14:07:45.691][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 14:07:45.692][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 14:07:45.696][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 14:07:45.697][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 14:07:45.698][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 14:07:45.699][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 14:07:45.700][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:45.701][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 14:07:45.702][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 14:07:45.704][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 14:07:45.707][biodb::testThat]
biodb.INFO [2025-08-29 14:07:45.708][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-08-29 14:07:45.709][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 14:07:45.710][biodb::testThat]
biodb.DEBUG[2025-08-29 14:07:45.713][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 14:07:45.719][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:45.721][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 14:07:45.722][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:45.724][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 14:07:45.727][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 14:07:45.731][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 14:07:45.732][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-08-29 14:07:45.733][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:45.735][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-08-29 14:07:45.739][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-08-29 14:07:45.741][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 14:07:45.742][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-08-29 14:07:45.743][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 14:07:45.747][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2025-08-29 14:07:45.749][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 14:07:45.750][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 14:07:45.751][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 14:07:45.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 14:07:45.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.764][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[2025-08-29 14:07:45.770][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.771][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.773][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.779][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:45.780][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:45.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.781][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.783][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 14:07:45.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 14:07:45.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.786][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:45.787][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:45.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.789][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 14:07:45.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 14:07:45.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.794][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 14:07:45.795][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 14:07:45.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.796][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.798][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 14:07:45.799][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 14:07:45.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.801][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.802][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:45.803][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:45.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.806][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.808][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:45.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 14:07:45.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.812][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:45.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:45.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.815][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.826][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 14:07:45.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 14:07:45.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:45.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:45.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.833][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:45.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 14:07:45.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.838][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:45.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:45.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.840][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 14:07:45.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 14:07:45.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.845][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:45.846][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:45.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.848][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.849][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 14:07:45.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 14:07:45.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.852][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:45.853][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:45.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.855][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.856][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 14:07:45.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 14:07:45.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:45.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:45.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:45.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:45.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 14:07:45.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 14:07:45.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 14:07:45.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 14:07:45.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 14:07:45.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 14:07:45.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 14:07:45.902][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-08-29 14:07:45.906][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 14:07:45.907][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 14:07:45.908][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 14:07:45.909][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 14:07:45.910][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 14:07:45.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 14:07:45.911][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 14:07:45.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 14:07:45.913][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 14:07:45.913][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 384 ]
> 
> proc.time()
   user  system elapsed 
 19.492   1.348  26.883

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.6651.1475.380
ChebiEntry0.3580.0200.388