| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-29 11:37 -0400 (Mon, 29 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
| 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 206/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.14.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: biodbChebi |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbChebi_1.14.0.tar.gz |
| StartedAt: 2025-09-28 21:24:55 -0400 (Sun, 28 Sep 2025) |
| EndedAt: 2025-09-28 21:26:55 -0400 (Sun, 28 Sep 2025) |
| EllapsedTime: 120.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbChebi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbChebi_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘biodbChebi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ChebiConn
> ### Title: ChEBI connector class.
> ### Aliases: ChebiConn
>
> ### ** Examples
>
> # Create an instance with default settings:
> mybiodb <- biodb::newInst()
INFO [21:25:51.446] Loading definitions from package biodb version 1.16.0.
INFO [21:25:51.859] Loading definitions from package biodbChebi version 1.14.0.
>
> # Create a connector
> conn <- mybiodb$getFactory()$createConn('chebi')
>
> # Get an entry
> e <- conn$getEntry('15440')
>
> # Convert an InChI KEY to a ChEBI identifier
> conn$convInchiToChebi('YYGNTYWPHWGJRM-AAJYLUCBSA-N')
INFO [21:25:53.588] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:25:54.454] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:25:55.306] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:25:56.073] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:25:56.926] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:25:57.782] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:25:58.699] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:25:59.580] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:26:00.353] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
INFO [21:26:01.128] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=YYGNTYWPHWGJRM-AAJYLUCBSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". Retrying connection to server...
Error in if (file == "" || length(file) == 0) stop("empty or no content specified") :
missing value where TRUE/FALSE needed
Calls: <Anonymous> -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─conn$annotateMzValues(...)
4. └─self$searchForEntries(fieldsFilter, max.results = max.results)
5. └─private$doSearchForEntries(fields = fields, max.results = max.results)
6. └─private$searchByMass(...)
7. └─self$wsGetLiteEntity(...)
8. └─XML::xmlInternalTreeParse(results, asText = TRUE)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 179 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck/00check.log’
for details.
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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)
biodbChebi.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-09-28 21:26:03.508][biodb::testContext]
biodb.INFO [2025-09-28 21:26:03.510][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:03.523][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-09-28 21:26:03.524][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:03.525][biodb::testContext]
biodb.INFO [2025-09-28 21:26:03.531][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:03.533][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:03.540][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:03.541][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-28 21:26:03.542][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-28 21:26:03.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.545][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-28 21:26:03.563][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-28 21:26:03.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.567][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-28 21:26:03.568][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-28 21:26:03.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.572][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-28 21:26:03.573][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-28 21:26:03.574][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-28 21:26:03.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.578][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-28 21:26:03.579][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-28 21:26:03.580][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-28 21:26:03.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.583][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-28 21:26:03.584][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-28 21:26:03.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.588][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-28 21:26:03.589][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-28 21:26:03.590][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-28 21:26:03.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.594][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-28 21:26:03.595][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-28 21:26:03.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.598][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-28 21:26:03.599][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-28 21:26:03.600][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-28 21:26:03.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.603][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[2025-09-28 21:26:03.604][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:03.605][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-28 21:26:03.606][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-28 21:26:03.607][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-28 21:26:03.608][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-28 21:26:03.609][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-28 21:26:03.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.612][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-28 21:26:03.613][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-28 21:26:03.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.616][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[2025-09-28 21:26:03.617][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-28 21:26:03.618][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-28 21:26:03.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.622][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-28 21:26:03.623][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-28 21:26:03.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.627][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-28 21:26:03.628][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-28 21:26:03.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.631][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-28 21:26:03.632][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-28 21:26:03.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.636][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:03.637][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-28 21:26:03.640][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-28 21:26:03.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.644][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-28 21:26:03.645][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-28 21:26:03.646][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-28 21:26:03.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.649][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[2025-09-28 21:26:03.652][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-28 21:26:03.685][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.700][self$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[2025-09-28 21:26:03.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.709][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:03.710][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.711][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.712][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.713][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.714][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:03.714][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:03.715][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.716][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-28 21:26:03.717][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:03.718][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.719][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.720][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:03.720][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:03.720][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:03.720][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:03.720][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:03.721][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:03.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.730][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.731][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:03.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.734][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.735][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.736][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:03.737][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:03.739][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.740][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.741][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-28 21:26:03.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.745][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:03.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.747][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:03.748][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.749][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.750][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.752][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.753][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:03.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:03.755][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.756][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-28 21:26:03.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:03.758][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.759][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:03.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:03.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:03.760][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:03.760][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:03.762][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:03.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.764][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.765][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:03.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.768][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.769][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:03.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:03.772][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.773][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.774][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-28 21:26:03.776][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.777][self$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[2025-09-28 21:26:03.778][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:03.781][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.783][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.784][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.785][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:03.786][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:03.787][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.788][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-28 21:26:03.789][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:03.790][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.791][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.793][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.794][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:03.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:03.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.800][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.801][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.802][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:03.803][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:03.804][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.805][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.806][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-28 21:26:03.808][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.810][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:03.811][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:03.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.815][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.816][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.817][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:03.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:03.819][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.820][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-28 21:26:03.821][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:03.822][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.824][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:03.825][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.826][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:03.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:03.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:03.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:03.832][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:03.833][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:03.835][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:03.836][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:03.837][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:03.842][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:03.843][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.878][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[2025-09-28 21:26:03.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.887][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.DEBUG[2025-09-28 21:26:03.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.897][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[2025-09-28 21:26:03.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.923][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.DEBUG[2025-09-28 21:26:03.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:03.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.932][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[2025-09-28 21:26:03.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:03.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:03.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:03.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:03.937][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[2025-09-28 21:26:03.938][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-28 21:26:03.942][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-28 21:26:03.943][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-28 21:26:03.945][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-28 21:26:03.946][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:03.947][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-28 21:26:03.949][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:03.950][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:03.951][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-28 21:26:03.953][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-28 21:26:03.954][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:03.955][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-28 21:26:03.957][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:03.958][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:03.959][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-28 21:26:03.961][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-28 21:26:03.962][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-28 21:26:03.964][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-28 21:26:03.965][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:03.966][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-28 21:26:03.968][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-28 21:26:03.969][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-28 21:26:03.970][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-28 21:26:03.972][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-28 21:26:03.973][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-28 21:26:03.974][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-28 21:26:03.976][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-28 21:26:03.977][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-28 21:26:03.978][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-28 21:26:03.980][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-28 21:26:03.981][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-28 21:26:03.982][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-28 21:26:03.984][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-28 21:26:03.985][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-28 21:26:03.986][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-28 21:26:03.988][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-28 21:26:03.989][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-28 21:26:03.990][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-28 21:26:03.992][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-28 21:26:03.993][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-28 21:26:03.994][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-28 21:26:03.996][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-28 21:26:03.997][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-28 21:26:03.998][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-28 21:26:04.000][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-28 21:26:04.001][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-28 21:26:04.003][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-28 21:26:04.004][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-28 21:26:04.005][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-28 21:26:04.007][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-28 21:26:04.008][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-28 21:26:04.009][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-28 21:26:04.011][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-28 21:26:04.012][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-28 21:26:04.013][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-28 21:26:04.015][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-28 21:26:04.016][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-28 21:26:04.017][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-28 21:26:04.019][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-28 21:26:04.020][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-28 21:26:04.021][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-28 21:26:04.023][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-28 21:26:04.024][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-28 21:26:04.025][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-28 21:26:04.027][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-28 21:26:04.028][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-28 21:26:04.029][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:04.031][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:04.032][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-28 21:26:04.033][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-28 21:26:04.035][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-28 21:26:04.036][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-28 21:26:04.037][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-28 21:26:04.039][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-28 21:26:04.040][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-28 21:26:04.041][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-28 21:26:04.043][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-28 21:26:04.044][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-28 21:26:04.045][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-28 21:26:04.047][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-28 21:26:04.048][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-28 21:26:04.049][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-28 21:26:04.051][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-28 21:26:04.057][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-28 21:26:04.058][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:04.061][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:04.062][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.064][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.075][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.DEBUG[2025-09-28 21:26:04.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.081][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.DEBUG[2025-09-28 21:26:04.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.141][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[2025-09-28 21:26:04.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.171][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[2025-09-28 21:26:04.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:04.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:04.179][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:04.188][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-28 21:26:04.190][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:04.191][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-28 21:26:04.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:04.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:04.194][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:04.195][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:04.196][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:04.197][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-28 21:26:04.198][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-28 21:26:04.199][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:04.200][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:04.201][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-28 21:26:04.202][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-28 21:26:04.203][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-28 21:26:04.204][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:04.205][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:04.205][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:04.205][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:04.206][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-28 21:26:04.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:04.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:04.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:04.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:04.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:04.212][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:04.213][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-28 21:26:04.213][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-28 21:26:04.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:04.214][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:04.215][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:04.216][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-28 21:26:04.216][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-28 21:26:04.222][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:04.224][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:04.226][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-28 21:26:04.227][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:04.228][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:04.230][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:04.252][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-28 21:26:04.253][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-28 21:26:04.257][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-28 21:26:04.261][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-28 21:26:04.299][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:04.300][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:04.302][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-28 21:26:04.303][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-28 21:26:04.311][biodb::testThat]
biodb.INFO [2025-09-28 21:26:04.312][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-09-28 21:26:04.313][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:04.314][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:04.317][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-09-28 21:26:04.319][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-28 21:26:04.322][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:04.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:04.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:04.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:04.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:04.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:04.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:04.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:04.356][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.357][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.359][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.376][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:04.377][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:04.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.379][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.405][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:04.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:04.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.410][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:04.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:04.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.412][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:04.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:04.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.418][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:04.419][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:04.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.421][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:04.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:04.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.426][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.427][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.429][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.434][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.435][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.437][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.438][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.442][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:04.443][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.445][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.446][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:04.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.450][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.453][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.466][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:04.467][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:04.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.469][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:04.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:04.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.474][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:04.475][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.477][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.478][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:04.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.482][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:04.483][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:04.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.485][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.486][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:04.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:04.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:04.562][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-09-28 21:26:04.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:04.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:04.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:04.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:04.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-28 21:26:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-28 21:26:04.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.618][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-28 21:26:04.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-28 21:26:04.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.622][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-28 21:26:04.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-28 21:26:04.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.626][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-28 21:26:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-28 21:26:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.723][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.724][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.726][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:04.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:04.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.756][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.758][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:04.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:04.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:04.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:04.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:04.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:04.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:04.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.782][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:04.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:04.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.785][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:04.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:04.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:04.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:04.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.801][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:04.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:04.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.805][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:04.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:04.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.809][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:04.810][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:04.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.812][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.813][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:04.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:04.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.835][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.836][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.838][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:04.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.862][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.863][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.865][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:04.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:04.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:04.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.885][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:04.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:04.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.889][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:04.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:04.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.893][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:04.894][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:04.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.896][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.897][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:04.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:04.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.908][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.912][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.916][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.920][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.921][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.923][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.924][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:04.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.935][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.943][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.947][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.948][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.950][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.951][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:04.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:04.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:04.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.966][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:04.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:04.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.970][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:04.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:04.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.974][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:04.975][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:04.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.976][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.977][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:04.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:04.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:04.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:04.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:04.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.000][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.001][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.003][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.031][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.032][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.034][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.047][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.050][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.054][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:05.055][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:05.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.057][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.061][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:05.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:05.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.064][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.068][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.069][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.071][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.075][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.078][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:05.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:05.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.085][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.089][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.090][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.092][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.096][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.097][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.099][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.103][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-09-28 21:26:05.104][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:05.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.106][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.110][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.113][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.117][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:05.118][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:05.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.120][ef$get] fields variable is a list.
biodb.INFO [2025-09-28 21:26:05.127][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.128][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-28 21:26:05.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:05.129][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:05.143][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-09-28 21:26:05.149][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-28 21:26:05.154][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-09-28 21:26:05.155][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:05.161][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-09-28 21:26:05.162][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-28 21:26:05.185][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-28 21:26:05.187][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:05.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:05.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:05.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:05.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:05.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:05.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:05.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:05.199][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.200][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.202][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.223][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:05.224][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:05.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.226][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.228][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:05.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:05.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.232][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:05.233][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:05.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.234][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.236][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:05.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:05.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.240][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.241][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.242][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.248][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.249][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.251][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.256][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:05.257][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:05.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.258][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.260][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:05.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:05.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.264][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:05.265][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.267][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.268][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:05.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.272][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.273][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.275][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.280][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.285][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.287][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.288][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.292][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:05.293][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:05.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.295][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.296][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:05.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:05.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.300][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:05.301][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:05.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.303][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.304][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:05.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:05.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:05.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:05.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:05.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:05.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:05.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:05.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:05.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:05.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:05.347][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-09-28 21:26:05.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-09-28 21:26:05.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-09-28 21:26:05.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-09-28 21:26:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-09-28 21:26:05.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-09-28 21:26:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-09-28 21:26:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-28 21:26:05.367][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.368][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-28 21:26:05.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:05.370][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:05.373][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.374][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.376][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:05.377][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-09-28 21:26:05.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:05.421][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-09-28 21:26:05.426][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-28 21:26:05.446][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:05.462][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-28 21:26:05.463][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:05.465][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-28 21:26:05.488][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:05.491][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:05.493][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-28 21:26:05.494][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:05.495][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-09-28 21:26:05.497][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-09-28 21:26:05.508][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:05.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.511][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.512][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.513][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.515][ef$get] fields variable is a list.
biodb.INFO [2025-09-28 21:26:05.519][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.520][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-09-28 21:26:05.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:05.522][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:05.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:05.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:05.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:05.617][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:05.620][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:05.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-28 21:26:05.622][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:05.624][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-09-28 21:26:05.637][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.639][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-09-28 21:26:05.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:05.640][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.687][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.691][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.695][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-28 21:26:05.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-28 21:26:05.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.699][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-28 21:26:05.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-28 21:26:05.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:05.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:05.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:05.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.746][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-28 21:26:05.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.750][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-28 21:26:05.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-28 21:26:05.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:05.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-28 21:26:05.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-28 21:26:05.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-09-28 21:26:05.763][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.764][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-28 21:26:05.765][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:05.766][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.773][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.774][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-28 21:26:05.775][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:05.775][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.783][biodb::testThat]
biodb.INFO [2025-09-28 21:26:05.784][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-28 21:26:05.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:05.786][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:05.789][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-09-28 21:26:06.353][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-09-28 21:26:07.390][biodb::testThat]
biodb.INFO [2025-09-28 21:26:07.391][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-28 21:26:07.392][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:07.393][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:07.757][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[2025-09-28 21:26:08.113][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:08.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:08.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.118][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.120][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:08.121][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:08.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.124][ef$get] fields variable is a list.
biodb.INFO [2025-09-28 21:26:08.127][biodb::testThat]
biodb.INFO [2025-09-28 21:26:08.129][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-09-28 21:26:08.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:08.132][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:08.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:08.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:08.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:08.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:08.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:08.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:08.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:08.255][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:08.259][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:08.260][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-28 21:26:08.261][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:08.263][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-09-28 21:26:08.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:08.333][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:08.334][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-09-28 21:26:08.336][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:08.343][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-09-28 21:26:08.357][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-28 21:26:08.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-28 21:26:08.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:08.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:08.399][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:08.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-09-28 21:26:08.401][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:08.403][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-09-28 21:26:08.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:08.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:08.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:08.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:08.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:08.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:08.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:08.417][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-09-28 21:26:08.475][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-28 21:26:08.477][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-09-28 21:26:08.478][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:08.480][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml".
biodb.DEBUG[2025-09-28 21:26:08.481][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-28 21:26:08.482][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-28 21:26:08.484][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:08.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:08.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:08.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:08.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:08.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:08.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:08.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:08.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:08.532][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-09-28 21:26:08.533][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-09-28 21:26:08.551][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[2025-09-28 21:26:08.554][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:08.556][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-09-28 21:26:08.557][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:08.559][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-09-28 21:26:08.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:08.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:08.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:08.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:08.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:08.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:08.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:08.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:08.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:08.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:08.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:08.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:08.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:08.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:08.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:08.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:08.614][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-09-28 21:26:08.616][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-28 21:26:08.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-09-28 21:26:08.619][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:08.620][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml".
biodb.DEBUG[2025-09-28 21:26:08.621][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-28 21:26:08.623][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-28 21:26:08.624][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:08.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:08.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:08.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:08.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:08.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:08.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:08.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:08.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:08.679][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-09-28 21:26:08.680][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-09-28 21:26:08.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:08.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:08.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:08.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:08.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:08.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:08.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:08.693][private$loadEntries] Creating entries from ids [1]: "227078".
biodb.DEBUG[2025-09-28 21:26:08.694][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-28 21:26:08.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "227078".
biodb.TRACE[2025-09-28 21:26:08.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:08.698][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/227078.xml".
biodb.DEBUG[2025-09-28 21:26:08.700][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-28 21:26:08.701][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-28 21:26:08.702][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:08.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:08.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:08.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:08.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:08.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:08.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:08.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:08.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:08.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:08.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:08.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:08.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:08.751][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-09-28 21:26:08.752][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-09-28 21:26:08.754][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:08.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:08.758][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:08.760][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:09.089][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:09.099][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:09.101][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:09.103][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:09.552][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:09.557][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:09.560][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:09.596][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:09.934][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:09.937][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:09.941][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:09.946][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:10.382][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:10.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:10.386][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:10.390][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:10.721][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:10.723][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:10.726][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:10.729][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:11.165][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:11.168][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:11.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:11.176][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:11.510][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:11.512][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:11.514][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:11.516][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:12.039][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:12.042][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:12.046][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:12.052][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:12.388][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:12.390][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:12.394][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:12.397][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:12.831][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:12.835][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:12.838][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:12.843][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:13.177][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:13.179][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:13.183][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:13.187][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:13.623][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:13.626][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:13.629][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:13.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:13.970][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:13.972][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:13.976][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:13.980][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:14.415][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:14.507][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:14.511][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:14.514][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:14.845][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:14.847][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:14.851][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:14.854][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:15.391][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:15.395][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:15.399][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:15.405][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:15.740][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:15.742][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:15.746][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:15.750][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:16.277][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:16.280][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:16.283][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:16.288][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:16.624][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:16.625][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:16.627][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:16.630][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:17.155][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.INFO [2025-09-28 21:26:17.202][biodb::testThat]
biodb.INFO [2025-09-28 21:26:17.205][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-09-28 21:26:17.207][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:17.209][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:17.216][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-28 21:26:17.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-28 21:26:17.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:17.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:17.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:17.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:17.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:17.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:17.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:17.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:17.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:17.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:17.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:17.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:17.294][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[2025-09-28 21:26:17.298][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:17.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-09-28 21:26:17.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:17.302][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-09-28 21:26:17.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:17.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:17.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:17.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:17.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:17.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:17.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:17.316][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[2025-09-28 21:26:17.319][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:17.321][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-09-28 21:26:17.322][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:17.323][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-09-28 21:26:17.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:17.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:17.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:17.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:17.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:17.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:17.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:17.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:17.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:17.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:17.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:17.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:17.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:17.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:17.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:17.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:17.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:17.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:17.357][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[2025-09-28 21:26:17.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:17.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:17.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:17.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:17.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:17.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:17.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:17.406][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:17.422][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:17.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:17.425][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:17.755][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:17.756][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:17.758][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:17.760][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:18.482][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:18.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:18.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:18.491][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:18.827][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:18.829][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:18.832][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:18.834][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:19.267][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:19.270][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:19.272][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:19.275][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:19.608][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:19.610][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:19.612][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:19.615][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:20.077][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:20.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:20.082][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:20.087][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:20.420][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:20.423][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:20.426][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:20.430][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:20.866][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:20.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:20.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:20.875][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:21.209][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:21.212][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:21.215][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:21.218][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:21.650][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:21.652][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:21.654][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:21.657][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:21.988][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:21.990][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:21.993][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:21.996][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:22.430][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:22.433][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:22.435][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:22.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:22.798][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:22.800][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:22.804][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:22.807][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:23.239][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:23.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:23.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:23.244][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:23.576][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:23.579][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:23.582][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:23.585][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:24.019][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:24.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:24.024][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:24.029][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:24.380][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:24.385][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:24.390][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:24.394][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:24.834][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:24.838][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:24.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:24.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:25.189][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:25.190][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:25.192][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:25.195][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:25.721][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.INFO [2025-09-28 21:26:25.797][biodb::testThat]
biodb.INFO [2025-09-28 21:26:25.799][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-09-28 21:26:25.800][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:25.801][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:25.806][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-28 21:26:25.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-28 21:26:25.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:25.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:25.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:25.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:25.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:25.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:25.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:25.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:25.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:25.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:25.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:25.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:25.924][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[2025-09-28 21:26:25.927][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:25.929][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-09-28 21:26:25.930][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:25.931][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-09-28 21:26:25.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:25.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:25.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:25.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:25.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:25.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:25.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:25.950][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[2025-09-28 21:26:25.953][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:25.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-09-28 21:26:25.956][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:25.957][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-09-28 21:26:25.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:25.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:25.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:25.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:25.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:25.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:25.969][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[2025-09-28 21:26:25.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:25.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:25.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:25.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:25.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:25.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:25.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:25.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:25.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:25.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:25.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:25.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:25.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:25.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:25.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:26.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:26.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:26.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:26.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:26.005][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:26.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:26.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:26.011][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:26.340][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:26.342][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:26.345][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:26.347][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:26.781][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:26.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:26.785][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:26.789][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:27.120][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:27.122][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:27.126][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:27.129][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:27.562][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:27.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:27.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:27.572][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:27.904][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:27.907][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:27.925][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:27.930][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:28.458][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:28.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:28.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:28.468][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:28.802][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:28.804][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:28.808][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:28.811][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:29.247][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:29.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:29.252][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:29.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:29.590][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:29.592][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:29.595][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:29.598][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:30.029][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:30.030][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:30.032][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:30.034][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:30.362][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:30.364][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:30.365][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:30.367][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:30.889][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:30.892][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:30.894][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:30.898][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:31.234][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:31.236][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:31.237][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:31.239][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:31.676][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:31.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:31.681][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:31.685][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:32.019][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:32.021][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:32.024][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:32.028][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:32.460][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:32.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:32.465][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:32.469][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:32.800][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:32.802][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:32.804][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:32.805][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:33.328][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:33.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:33.333][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:33.338][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:33.675][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:33.676][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:33.678][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:33.680][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:34.110][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.INFO [2025-09-28 21:26:34.157][biodb::testThat]
biodb.INFO [2025-09-28 21:26:34.159][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-09-28 21:26:34.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:34.161][biodb::testThat]
biodb.TRACE[2025-09-28 21:26:34.165][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-28 21:26:34.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-28 21:26:34.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:34.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:34.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:34.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:34.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:34.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:34.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:34.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:34.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:34.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:34.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:34.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:34.209][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[2025-09-28 21:26:34.212][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:34.213][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-09-28 21:26:34.215][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:34.216][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-09-28 21:26:34.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:34.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:34.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:34.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:34.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:34.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:34.229][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[2025-09-28 21:26:34.231][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[2025-09-28 21:26:34.234][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:34.235][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-09-28 21:26:34.237][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:34.238][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-09-28 21:26:34.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:34.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:34.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:34.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:34.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:34.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:34.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:34.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:34.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:34.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:34.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:34.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:34.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:34.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:34.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:34.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:34.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:34.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:34.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:34.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:34.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:34.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:34.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:34.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:34.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:34.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:34.295][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-09-28 21:26:34.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:34.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:34.302][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:34.630][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:34.632][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:34.633][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:34.635][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:35.154][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:35.156][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:35.157][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:35.159][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:35.488][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:35.490][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:35.491][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:35.493][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:36.024][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:36.026][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:36.027][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:36.029][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:36.358][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:36.360][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:36.362][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:36.365][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:36.901][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:36.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:36.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:36.911][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:37.290][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:37.292][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:37.295][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:37.297][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:37.826][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:37.828][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:37.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:37.835][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:38.171][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:38.173][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:38.176][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:38.180][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:38.614][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:38.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:38.619][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:38.622][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:38.957][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:38.960][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:38.963][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:38.967][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:39.400][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:39.424][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:39.427][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:39.430][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:39.761][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:39.764][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:39.767][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:39.770][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:40.323][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:40.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:40.328][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:40.332][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:40.668][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:40.669][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:40.672][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:40.674][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:41.104][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:41.105][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:41.107][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:41.109][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:41.443][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:41.446][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:41.450][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:41.454][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:41.888][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-09-28 21:26:41.891][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-09-28 21:26:41.894][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-09-28 21:26:41.898][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-09-28 21:26:42.232][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-09-28 21:26:42.234][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-09-28 21:26:42.237][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-09-28 21:26:42.239][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.INFO [2025-09-28 21:26:42.675][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.INFO [2025-09-28 21:26:42.708][biodb::testThat]
biodb.INFO [2025-09-28 21:26:42.711][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-09-28 21:26:42.713][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:42.715][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:42.719][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-09-28 21:26:42.721][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-28 21:26:42.724][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-09-28 21:26:42.727][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:42.729][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2025-09-28 21:26:42.731][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-28 21:26:42.734][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-28 21:26:42.736][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:42.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:42.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:42.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:42.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:42.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:42.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:42.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:42.758][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.759][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.762][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.785][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:42.787][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:42.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.790][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.791][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:42.792][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:42.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.794][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.796][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:42.797][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:42.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.799][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.801][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:42.802][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:42.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.804][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.805][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:42.807][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:42.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.809][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.810][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:42.811][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:42.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.813][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.815][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:42.816][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:42.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.818][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.819][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:42.820][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:42.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.822][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.823][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:42.825][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:42.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.827][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:42.829][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:42.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.831][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:42.874][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-09-28 21:26:42.875][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-09-28 21:26:42.884][biodb::testThat]
biodb.INFO [2025-09-28 21:26:42.892][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-09-28 21:26:42.893][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:42.894][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:42.905][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-09-28 21:26:42.907][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-09-28 21:26:42.908][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-09-28 21:26:42.910][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-09-28 21:26:42.911][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-09-28 21:26:42.914][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2025-09-28 21:26:42.915][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-28 21:26:42.917][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-09-28 21:26:42.918][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:42.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:42.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:42.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:42.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:42.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:42.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:42.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:42.932][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.933][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.935][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:42.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:42.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.941][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:42.942][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:42.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.944][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.945][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:42.946][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:42.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.948][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.950][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:42.951][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:42.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.953][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.954][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:42.955][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:42.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.957][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.958][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:42.959][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:42.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.962][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.963][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:42.964][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:42.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.966][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:42.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:42.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.970][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.972][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:42.973][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:42.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.975][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.976][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:42.977][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:42.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.979][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.981][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:42.982][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:42.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.984][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:42.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:42.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:42.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:43.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:43.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:43.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:43.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:43.036][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.037][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.039][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.045][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:43.046][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:43.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.048][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.049][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:43.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:43.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.054][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:43.057][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:43.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.059][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.061][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:43.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:43.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.065][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:43.066][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:43.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.068][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:43.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:43.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.074][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.075][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.077][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.083][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.084][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.086][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.087][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.092][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:43.093][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:43.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.095][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:43.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:43.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.107][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.109][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.111][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.116][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:43.117][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:43.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.119][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:43.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:43.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:43.126][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:43.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.128][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.130][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:43.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:43.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.134][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:43.135][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:43.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.137][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.138][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:43.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:43.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:43.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:43.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:43.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:43.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:43.187][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.188][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.190][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.196][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:43.197][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:43.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.199][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.201][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.206][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:43.214][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:43.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.217][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:43.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:43.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.222][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:43.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:43.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.225][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:43.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:43.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.231][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.234][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:43.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.240][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.241][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.243][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.244][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:43.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.249][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:43.250][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:43.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.252][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.253][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:43.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:43.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.261][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.267][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:43.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:43.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.270][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:43.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:43.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:43.277][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:43.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.279][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.280][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:43.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:43.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.284][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:43.285][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:43.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.287][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.288][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:43.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:43.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:43.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:43.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:43.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:43.368][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-09-28 21:26:43.369][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-09-28 21:26:43.370][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-09-28 21:26:43.383][biodb::testThat]
biodb.INFO [2025-09-28 21:26:43.385][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-09-28 21:26:43.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:43.387][biodb::testThat]
biodb.INFO [2025-09-28 21:26:43.416][biodb::testThat]
biodb.INFO [2025-09-28 21:26:43.418][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-09-28 21:26:43.419][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:43.419][biodb::testThat]
biodb.INFO [2025-09-28 21:26:43.427][biodb::testThat]
biodb.INFO [2025-09-28 21:26:43.429][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-09-28 21:26:43.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:43.430][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:43.433][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[2025-09-28 21:26:43.437][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:43.438][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2025-09-28 21:26:43.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:43.441][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2025-09-28 21:26:43.453][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:43.454][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:43.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.457][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:43.458][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.459][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:43.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:43.461][ef$get] fields variable is a list.
biodb.INFO [2025-09-28 21:26:43.462][biodb::testThat]
biodb.INFO [2025-09-28 21:26:43.463][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-09-28 21:26:43.465][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:43.466][biodb::testThat]
biodb.ERROR[2025-09-28 21:26:43.480][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-09-28 21:26:43.496][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-09-28 21:26:43.509][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-28 21:26:43.510][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-28 21:26:43.517][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-28 21:26:43.518][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-28 21:26:43.519][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:43.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:43.521][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.523][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-28 21:26:43.534][biodb::testContext]
biodb.INFO [2025-09-28 21:26:43.535][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:43.536][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-09-28 21:26:43.537][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:43.538][biodb::testContext]
biodb.INFO [2025-09-28 21:26:43.540][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:43.542][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:43.546][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:43.547][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-28 21:26:43.548][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-28 21:26:43.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.552][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-28 21:26:43.553][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-28 21:26:43.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.557][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-28 21:26:43.558][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-28 21:26:43.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.562][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-28 21:26:43.563][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-28 21:26:43.564][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-28 21:26:43.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.568][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-28 21:26:43.569][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-28 21:26:43.570][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-28 21:26:43.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.574][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-28 21:26:43.575][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-28 21:26:43.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.579][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-28 21:26:43.580][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-28 21:26:43.581][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-28 21:26:43.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.585][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-28 21:26:43.586][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-28 21:26:43.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.589][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-28 21:26:43.590][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-28 21:26:43.591][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-28 21:26:43.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.595][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:43.596][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-28 21:26:43.597][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-28 21:26:43.598][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-28 21:26:43.599][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-28 21:26:43.600][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-28 21:26:43.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.603][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-28 21:26:43.604][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-28 21:26:43.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.616][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-28 21:26:43.617][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-28 21:26:43.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.621][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-28 21:26:43.622][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-28 21:26:43.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.626][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-28 21:26:43.627][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-28 21:26:43.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.630][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[2025-09-28 21:26:43.631][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-28 21:26:43.632][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-28 21:26:43.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.635][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:43.636][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-28 21:26:43.640][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-28 21:26:43.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.643][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-28 21:26:43.644][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-28 21:26:43.645][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-28 21:26:43.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.649][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-28 21:26:43.651][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.652][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-28 21:26:43.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.655][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:43.656][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.657][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.658][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.659][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.660][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:43.661][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:43.662][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.663][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-28 21:26:43.664][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:43.665][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.666][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.667][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:43.667][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:43.667][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:43.667][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:43.667][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:43.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:43.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.672][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:43.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.676][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.677][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:43.677][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:43.678][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.679][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.681][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-28 21:26:43.682][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.683][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:43.684][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.685][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:43.686][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.687][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.688][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.689][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.690][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:43.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:43.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.693][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-28 21:26:43.695][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:43.696][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.697][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:43.697][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:43.697][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:43.697][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:43.697][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:43.699][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:43.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.701][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:43.702][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.703][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.704][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.705][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.706][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:43.707][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:43.713][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.714][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.716][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-28 21:26:43.718][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.719][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-28 21:26:43.720][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.721][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:43.722][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.723][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.724][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.725][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.726][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:43.727][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:43.728][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.729][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-28 21:26:43.730][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:43.731][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.732][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.733][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.734][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:43.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.737][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:43.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.740][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.741][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.742][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:43.743][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:43.744][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.745][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.746][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-28 21:26:43.748][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.750][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:43.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.752][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:43.753][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.755][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.757][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:43.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:43.759][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.760][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-28 21:26:43.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:43.762][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:43.764][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.765][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:43.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.769][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:43.770][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:43.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:43.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:43.773][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.773][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:43.774][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:43.775][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:43.776][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:43.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:43.779][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.793][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[2025-09-28 21:26:43.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.846][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[2025-09-28 21:26:43.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.855][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.DEBUG[2025-09-28 21:26:43.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:43.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:43.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:43.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:43.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:43.866][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-28 21:26:43.868][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-28 21:26:43.869][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-28 21:26:43.871][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-28 21:26:43.872][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:43.874][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-28 21:26:43.875][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:43.876][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:43.878][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-28 21:26:43.879][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-28 21:26:43.881][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:43.882][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-28 21:26:43.883][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:43.885][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:43.886][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-28 21:26:43.888][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-28 21:26:43.889][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-28 21:26:43.890][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-28 21:26:43.892][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:43.893][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-28 21:26:43.894][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-28 21:26:43.896][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-28 21:26:43.897][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-28 21:26:43.899][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-28 21:26:43.905][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-28 21:26:43.907][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-28 21:26:43.909][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-28 21:26:43.910][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-28 21:26:43.912][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-28 21:26:43.913][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-28 21:26:43.915][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-28 21:26:43.916][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-28 21:26:43.917][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-28 21:26:43.919][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-28 21:26:43.920][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-28 21:26:43.922][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-28 21:26:43.923][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-28 21:26:43.924][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-28 21:26:43.926][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-28 21:26:43.927][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-28 21:26:43.929][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-28 21:26:43.930][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-28 21:26:43.932][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-28 21:26:43.933][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-28 21:26:43.934][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-28 21:26:43.936][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-28 21:26:43.937][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-28 21:26:43.939][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-28 21:26:43.940][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-28 21:26:43.942][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-28 21:26:43.943][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-28 21:26:43.945][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-28 21:26:43.946][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-28 21:26:43.948][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-28 21:26:43.949][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-28 21:26:43.951][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-28 21:26:43.952][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-28 21:26:43.954][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-28 21:26:43.955][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-28 21:26:43.956][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-28 21:26:43.958][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-28 21:26:43.959][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-28 21:26:43.961][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-28 21:26:43.962][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-28 21:26:43.964][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-28 21:26:43.965][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-28 21:26:43.967][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:43.968][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:43.970][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-28 21:26:43.971][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-28 21:26:43.972][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-28 21:26:43.974][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-28 21:26:43.975][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-28 21:26:43.977][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-28 21:26:43.978][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-28 21:26:43.979][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-28 21:26:43.981][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-28 21:26:43.982][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-28 21:26:43.984][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-28 21:26:43.985][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-28 21:26:43.987][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-28 21:26:43.988][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-28 21:26:43.989][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-28 21:26:43.991][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-28 21:26:43.992][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:44.000][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:44.001][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.003][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.004][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[2025-09-28 21:26:44.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.030][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[2025-09-28 21:26:44.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.043][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[2025-09-28 21:26:44.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.301][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:44.302][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-28 21:26:44.304][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.305][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:44.308][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.309][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.311][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-28 21:26:44.312][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-28 21:26:44.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:44.314][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.314][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-28 21:26:44.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-28 21:26:44.316][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-28 21:26:44.318][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.319][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:44.319][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:44.319][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:44.320][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-28 21:26:44.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.322][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:44.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.325][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.326][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-28 21:26:44.326][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-28 21:26:44.327][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:44.328][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:44.329][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.330][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-28 21:26:44.330][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-28 21:26:44.331][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:44.333][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:44.335][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-28 21:26:44.336][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:44.338][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:44.339][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:44.343][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-28 21:26:44.344][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-28 21:26:44.345][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-28 21:26:44.346][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-28 21:26:44.348][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:44.349][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:44.350][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-28 21:26:44.351][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-28 21:26:44.353][biodb::testThat]
biodb.INFO [2025-09-28 21:26:44.354][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-09-28 21:26:44.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:44.355][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:44.359][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-28 21:26:44.363][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.364][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-28 21:26:44.365][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.366][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-28 21:26:44.370][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[2025-09-28 21:26:44.373][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.374][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-09-28 21:26:44.375][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.377][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-09-28 21:26:44.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.388][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[2025-09-28 21:26:44.390][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[2025-09-28 21:26:44.393][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-09-28 21:26:44.396][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.397][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-09-28 21:26:44.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.409][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[2025-09-28 21:26:44.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.446][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[2025-09-28 21:26:44.449][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-09-28 21:26:44.452][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.454][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-09-28 21:26:44.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.469][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[2025-09-28 21:26:44.472][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.474][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-09-28 21:26:44.475][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.477][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-09-28 21:26:44.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.490][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[2025-09-28 21:26:44.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.506][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[2025-09-28 21:26:44.509][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-09-28 21:26:44.512][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.513][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-09-28 21:26:44.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.528][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[2025-09-28 21:26:44.531][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.533][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-09-28 21:26:44.534][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.535][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-09-28 21:26:44.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.550][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[2025-09-28 21:26:44.553][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-09-28 21:26:44.556][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.558][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-09-28 21:26:44.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-28 21:26:44.578][biodb::testThat]
biodb.INFO [2025-09-28 21:26:44.579][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-09-28 21:26:44.580][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:44.581][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:44.584][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[2025-09-28 21:26:44.588][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.590][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2025-09-28 21:26:44.591][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.593][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2025-09-28 21:26:44.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.610][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[2025-09-28 21:26:44.614][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:44.615][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2025-09-28 21:26:44.617][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:44.618][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2025-09-28 21:26:44.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:44.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-28 21:26:44.637][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-28 21:26:44.638][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-28 21:26:44.640][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-28 21:26:44.641][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-28 21:26:44.641][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:44.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:44.643][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.646][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-28 21:26:44.651][biodb::testContext]
biodb.INFO [2025-09-28 21:26:44.652][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:44.653][biodb::testContext] Test context - Test web services
biodb.INFO [2025-09-28 21:26:44.654][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:44.655][biodb::testContext]
biodb.INFO [2025-09-28 21:26:44.658][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:44.660][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:44.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:44.665][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-28 21:26:44.666][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-28 21:26:44.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.670][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-28 21:26:44.671][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-28 21:26:44.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.674][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.DEBUG[2025-09-28 21:26:44.675][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-28 21:26:44.677][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-28 21:26:44.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.681][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-28 21:26:44.687][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-28 21:26:44.688][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-28 21:26:44.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.691][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[2025-09-28 21:26:44.692][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-28 21:26:44.693][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-28 21:26:44.694][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-28 21:26:44.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.697][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-28 21:26:44.698][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-28 21:26:44.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.701][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[2025-09-28 21:26:44.702][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-28 21:26:44.703][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-28 21:26:44.704][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-28 21:26:44.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.707][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-28 21:26:44.708][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-28 21:26:44.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.712][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-28 21:26:44.713][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-28 21:26:44.714][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-28 21:26:44.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.717][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:44.718][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-28 21:26:44.719][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-28 21:26:44.720][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-28 21:26:44.721][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-28 21:26:44.722][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-28 21:26:44.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.725][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[2025-09-28 21:26:44.725][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-28 21:26:44.726][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-28 21:26:44.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.730][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-28 21:26:44.731][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-28 21:26:44.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.734][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-28 21:26:44.736][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-28 21:26:44.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.739][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-28 21:26:44.740][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-28 21:26:44.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.744][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-28 21:26:44.745][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-28 21:26:44.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.749][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:44.750][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-28 21:26:44.753][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-28 21:26:44.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.756][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[2025-09-28 21:26:44.757][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-28 21:26:44.758][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-28 21:26:44.759][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-28 21:26:44.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.763][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-28 21:26:44.764][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.765][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-28 21:26:44.766][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.767][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:44.768][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.770][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.771][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.772][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:44.773][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:44.774][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.775][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-28 21:26:44.776][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:44.777][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.778][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.779][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:44.779][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:44.779][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:44.779][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:44.779][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:44.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:44.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.783][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:44.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.787][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.788][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:44.789][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:44.790][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.791][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.792][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-28 21:26:44.794][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.795][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:44.796][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.797][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:44.798][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.799][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.800][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.801][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.802][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:44.803][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:44.804][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.805][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-28 21:26:44.806][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:44.807][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.809][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:44.809][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:44.809][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:44.809][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:44.809][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:44.810][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:44.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.813][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:44.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.816][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.817][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.817][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:44.818][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:44.819][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.820][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.821][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-28 21:26:44.823][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.824][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-28 21:26:44.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.826][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:44.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.828][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.829][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.830][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.831][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:44.832][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:44.833][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.834][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-28 21:26:44.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:44.836][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.837][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.838][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.839][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:44.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.842][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:44.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.845][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.846][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.847][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:44.847][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:44.848][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.849][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.850][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-28 21:26:44.852][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.853][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:44.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.855][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:44.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.857][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.858][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.859][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.860][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:44.861][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:44.862][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.863][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-28 21:26:44.864][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:44.865][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.866][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:44.867][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.868][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:44.869][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.870][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:44.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:44.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:44.873][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:44.874][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.875][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:44.876][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:44.877][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:44.878][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:44.879][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:44.880][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.912][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.DEBUG[2025-09-28 21:26:44.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.925][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[2025-09-28 21:26:44.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.952][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[2025-09-28 21:26:44.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:44.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:44.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:44.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:44.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:44.957][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-28 21:26:44.959][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-28 21:26:44.960][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-28 21:26:44.962][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-28 21:26:44.963][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:44.964][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-28 21:26:44.966][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:44.967][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:44.969][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-28 21:26:44.970][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-28 21:26:44.971][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:44.973][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-28 21:26:44.974][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:44.975][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:44.977][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-28 21:26:44.978][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-28 21:26:44.980][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-28 21:26:44.981][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-28 21:26:44.982][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:44.984][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-28 21:26:44.985][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-28 21:26:44.986][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-28 21:26:44.988][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-28 21:26:44.989][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-28 21:26:44.990][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-28 21:26:44.992][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-28 21:26:44.993][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-28 21:26:44.995][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-28 21:26:44.996][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-28 21:26:44.997][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-28 21:26:44.999][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-28 21:26:45.000][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-28 21:26:45.001][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-28 21:26:45.003][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-28 21:26:45.004][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-28 21:26:45.005][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-28 21:26:45.007][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-28 21:26:45.008][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-28 21:26:45.010][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-28 21:26:45.011][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-28 21:26:45.012][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-28 21:26:45.014][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-28 21:26:45.015][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-28 21:26:45.016][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-28 21:26:45.018][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-28 21:26:45.019][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-28 21:26:45.021][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-28 21:26:45.022][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-28 21:26:45.023][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-28 21:26:45.025][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-28 21:26:45.026][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-28 21:26:45.034][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-28 21:26:45.036][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-28 21:26:45.037][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-28 21:26:45.038][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-28 21:26:45.040][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-28 21:26:45.041][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-28 21:26:45.042][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-28 21:26:45.044][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-28 21:26:45.045][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-28 21:26:45.046][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-28 21:26:45.048][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-28 21:26:45.049][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-28 21:26:45.050][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-28 21:26:45.052][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-28 21:26:45.053][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-28 21:26:45.054][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:45.056][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:45.057][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-28 21:26:45.058][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-28 21:26:45.060][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-28 21:26:45.061][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-28 21:26:45.062][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-28 21:26:45.064][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-28 21:26:45.065][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-28 21:26:45.066][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-28 21:26:45.067][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-28 21:26:45.069][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-28 21:26:45.070][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-28 21:26:45.071][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-28 21:26:45.073][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-28 21:26:45.074][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-28 21:26:45.075][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-28 21:26:45.077][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-28 21:26:45.078][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:45.079][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:45.080][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.082][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.089][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[2025-09-28 21:26:45.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.126][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[2025-09-28 21:26:45.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.133][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[2025-09-28 21:26:45.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.145][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[2025-09-28 21:26:45.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.158][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[2025-09-28 21:26:45.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.170][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[2025-09-28 21:26:45.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.182][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[2025-09-28 21:26:45.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.190][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:45.191][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-28 21:26:45.193][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.194][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:45.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.199][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.200][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-28 21:26:45.201][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-28 21:26:45.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:45.203][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.204][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-28 21:26:45.205][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-28 21:26:45.206][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-28 21:26:45.207][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.208][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:45.208][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:45.208][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:45.209][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-28 21:26:45.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:45.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.216][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-28 21:26:45.216][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-28 21:26:45.217][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:45.217][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:45.218][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.219][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-28 21:26:45.219][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-28 21:26:45.221][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:45.222][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:45.224][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-28 21:26:45.225][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:45.227][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:45.228][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:45.231][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-28 21:26:45.232][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-28 21:26:45.234][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-28 21:26:45.235][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-28 21:26:45.236][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:45.237][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:45.239][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-28 21:26:45.240][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-28 21:26:45.241][biodb::testThat]
biodb.INFO [2025-09-28 21:26:45.242][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-09-28 21:26:45.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:45.244][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:45.247][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-28 21:26:45.250][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:45.251][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-28 21:26:45.253][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:45.254][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-28 21:26:45.258][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[2025-09-28 21:26:45.261][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:45.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-09-28 21:26:45.263][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:45.265][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2025-09-28 21:26:45.272][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-28 21:26:45.273][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-28 21:26:45.274][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-28 21:26:45.275][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-28 21:26:45.276][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.278][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.280][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.280][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.INFO [2025-09-28 21:26:45.284][biodb::testContext]
biodb.INFO [2025-09-28 21:26:45.285][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:45.286][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-09-28 21:26:45.287][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-28 21:26:45.288][biodb::testContext]
biodb.INFO [2025-09-28 21:26:45.290][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:45.292][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:45.295][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:45.297][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-28 21:26:45.298][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-28 21:26:45.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.301][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-28 21:26:45.302][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-28 21:26:45.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.306][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-28 21:26:45.307][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-28 21:26:45.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.311][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-28 21:26:45.312][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-28 21:26:45.313][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-28 21:26:45.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.316][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-28 21:26:45.317][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-28 21:26:45.318][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-28 21:26:45.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.322][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-28 21:26:45.323][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-28 21:26:45.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.327][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-28 21:26:45.328][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-28 21:26:45.329][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-28 21:26:45.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.332][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-28 21:26:45.333][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-28 21:26:45.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.337][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-28 21:26:45.338][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-28 21:26:45.339][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-28 21:26:45.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.342][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:45.343][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-28 21:26:45.344][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-28 21:26:45.345][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-28 21:26:45.346][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-28 21:26:45.347][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-28 21:26:45.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.351][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-28 21:26:45.352][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-28 21:26:45.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.355][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-28 21:26:45.356][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-28 21:26:45.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.360][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-28 21:26:45.361][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-28 21:26:45.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.364][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-28 21:26:45.366][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-28 21:26:45.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.368][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[2025-09-28 21:26:45.369][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-28 21:26:45.370][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-28 21:26:45.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.374][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-28 21:26:45.375][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-28 21:26:45.379][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-28 21:26:45.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.382][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[2025-09-28 21:26:45.388][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-28 21:26:45.389][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-28 21:26:45.390][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-28 21:26:45.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.394][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-28 21:26:45.396][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.397][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-28 21:26:45.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.399][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:45.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.401][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.402][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.403][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.404][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:45.405][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:45.406][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.406][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-28 21:26:45.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:45.408][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.409][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.410][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:45.410][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:45.410][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:45.410][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:45.410][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:45.411][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:45.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.414][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:45.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.417][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.418][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.419][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:45.420][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:45.420][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.421][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.422][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-28 21:26:45.424][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.425][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:45.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:45.428][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.429][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.430][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.432][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:45.433][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:45.434][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.435][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-28 21:26:45.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:45.437][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.439][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:45.439][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:45.439][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:45.439][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-28 21:26:45.439][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-28 21:26:45.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:45.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.443][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:45.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.445][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.446][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:45.448][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:45.449][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.450][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.452][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-28 21:26:45.453][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.454][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-28 21:26:45.455][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.456][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:45.458][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.459][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.460][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.461][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.462][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-28 21:26:45.463][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:45.464][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.465][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-28 21:26:45.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:45.466][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.467][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.468][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.469][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:45.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.472][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:45.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.475][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.476][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:45.478][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:45.479][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.480][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.481][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-28 21:26:45.482][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.484][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-28 21:26:45.485][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.485][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:45.486][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.487][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.490][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.491][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-28 21:26:45.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:45.493][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.494][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-28 21:26:45.495][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:45.496][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.497][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.498][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.499][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-28 21:26:45.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:45.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.504][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.505][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:45.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:45.508][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.509][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-28 21:26:45.510][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:45.511][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.525][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[2025-09-28 21:26:45.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.534][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[2025-09-28 21:26:45.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.548][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[2025-09-28 21:26:45.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.574][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[2025-09-28 21:26:45.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.587][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[2025-09-28 21:26:45.588][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-28 21:26:45.589][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-28 21:26:45.590][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-28 21:26:45.592][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-28 21:26:45.593][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:45.594][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-28 21:26:45.596][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:45.597][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:45.599][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-28 21:26:45.600][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-28 21:26:45.601][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:45.603][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-28 21:26:45.604][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-28 21:26:45.605][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-28 21:26:45.607][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-28 21:26:45.608][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-28 21:26:45.609][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-28 21:26:45.611][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-28 21:26:45.612][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:45.613][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-28 21:26:45.615][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-28 21:26:45.616][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-28 21:26:45.617][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-28 21:26:45.619][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-28 21:26:45.620][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-28 21:26:45.621][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-28 21:26:45.623][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-28 21:26:45.624][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-28 21:26:45.626][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-28 21:26:45.627][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-28 21:26:45.628][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-28 21:26:45.630][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-28 21:26:45.631][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-28 21:26:45.632][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-28 21:26:45.634][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-28 21:26:45.635][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-28 21:26:45.636][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-28 21:26:45.638][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-28 21:26:45.639][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-28 21:26:45.640][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-28 21:26:45.642][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-28 21:26:45.643][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-28 21:26:45.645][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-28 21:26:45.646][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-28 21:26:45.647][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-28 21:26:45.649][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-28 21:26:45.650][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-28 21:26:45.651][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-28 21:26:45.653][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-28 21:26:45.654][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-28 21:26:45.655][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-28 21:26:45.657][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-28 21:26:45.658][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-28 21:26:45.660][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-28 21:26:45.661][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-28 21:26:45.662][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-28 21:26:45.664][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-28 21:26:45.665][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-28 21:26:45.666][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-28 21:26:45.668][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-28 21:26:45.669][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-28 21:26:45.671][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-28 21:26:45.672][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-28 21:26:45.673][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-28 21:26:45.675][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-28 21:26:45.676][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-28 21:26:45.677][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:45.679][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:45.680][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-28 21:26:45.681][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-28 21:26:45.683][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-28 21:26:45.684][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-28 21:26:45.685][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-28 21:26:45.687][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-28 21:26:45.688][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-28 21:26:45.689][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-28 21:26:45.691][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-28 21:26:45.692][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-28 21:26:45.694][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-28 21:26:45.695][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-28 21:26:45.696][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-28 21:26:45.698][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-28 21:26:45.699][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-28 21:26:45.700][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-28 21:26:45.702][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-28 21:26:45.703][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-28 21:26:45.704][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.706][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.707][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[2025-09-28 21:26:45.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.713][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[2025-09-28 21:26:45.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.719][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[2025-09-28 21:26:45.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.731][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[2025-09-28 21:26:45.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.756][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[2025-09-28 21:26:45.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.768][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[2025-09-28 21:26:45.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.793][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[2025-09-28 21:26:45.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-28 21:26:45.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-28 21:26:45.820][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-09-28 21:26:45.821][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-09-28 21:26:45.823][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.824][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.826][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-28 21:26:45.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.828][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.829][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.830][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-09-28 21:26:45.831][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-28 21:26:45.832][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-28 21:26:45.833][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.834][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-09-28 21:26:45.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-09-28 21:26:45.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-09-28 21:26:45.838][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-28 21:26:45.839][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-28 21:26:45.839][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-28 21:26:45.839][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-28 21:26:45.840][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-28 21:26:45.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.842][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-28 21:26:45.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-28 21:26:45.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-28 21:26:45.845][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-28 21:26:45.846][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-09-28 21:26:45.846][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-09-28 21:26:45.847][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-28 21:26:45.848][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-28 21:26:45.849][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-28 21:26:45.850][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-09-28 21:26:45.850][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-09-28 21:26:45.851][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-28 21:26:45.853][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-28 21:26:45.855][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-09-28 21:26:45.856][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-28 21:26:45.858][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-28 21:26:45.859][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-28 21:26:45.863][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-09-28 21:26:45.864][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-09-28 21:26:45.865][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-09-28 21:26:45.866][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-09-28 21:26:45.867][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:45.868][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-28 21:26:45.870][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-09-28 21:26:45.871][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-09-28 21:26:45.872][biodb::testThat]
biodb.INFO [2025-09-28 21:26:45.873][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-09-28 21:26:45.874][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-28 21:26:45.875][biodb::testThat]
biodb.DEBUG[2025-09-28 21:26:45.878][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-09-28 21:26:45.881][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:45.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-09-28 21:26:45.884][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:45.885][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-09-28 21:26:45.889][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[2025-09-28 21:26:45.892][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-09-28 21:26:45.893][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-09-28 21:26:45.894][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:45.896][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-09-28 21:26:45.900][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-09-28 21:26:45.901][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-09-28 21:26:45.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-09-28 21:26:45.904][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-09-28 21:26:45.906][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2025-09-28 21:26:45.907][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-09-28 21:26:45.908][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-09-28 21:26:45.910][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-09-28 21:26:45.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-28 21:26:45.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:45.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:45.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:45.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:45.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:45.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-28 21:26:45.925][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:45.926][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:45.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.928][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:45.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:45.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.933][ef$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:45.934][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:45.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.936][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.938][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-09-28 21:26:45.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-09-28 21:26:45.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.942][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:45.943][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:45.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.945][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.946][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-28 21:26:45.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-28 21:26:45.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.950][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-28 21:26:45.951][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-28 21:26:45.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.953][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.955][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-28 21:26:45.956][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-28 21:26:45.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.958][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.959][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:45.960][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:45.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.962][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.964][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:45.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-28 21:26:45.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.968][ef$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:45.969][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:45.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.971][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.973][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-09-28 21:26:45.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-28 21:26:45.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.977][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:45.978][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:45.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.980][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:45.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-28 21:26:45.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.985][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:45.987][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:45.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.988][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-28 21:26:45.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-28 21:26:45.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.994][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:45.995][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:45.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:45.997][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:45.999][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-09-28 21:26:46.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-09-28 21:26:46.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.003][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:46.004][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:46.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.006][ef$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.007][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-28 21:26:46.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-28 21:26:46.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:46.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:46.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:46.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:46.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:46.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:46.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-28 21:26:46.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-28 21:26:46.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:46.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:46.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:46.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:46.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:46.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:46.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:46.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:46.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:46.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:46.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-28 21:26:46.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-28 21:26:46.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-28 21:26:46.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-28 21:26:46.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-28 21:26:46.050][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-09-28 21:26:46.054][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-28 21:26:46.056][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-09-28 21:26:46.057][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-09-28 21:26:46.057][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-28 21:26:46.058][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-28 21:26:46.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-28 21:26:46.060][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-28 21:26:46.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-28 21:26:46.062][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-28 21:26:46.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 179 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_100_generic.R:16:1'): We can search for a compound ─────────────
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─db$searchCompound(...)
4. └─self$searchForEntries(fields, max.results = max.results)
5. └─private$doSearchForEntries(fields = fields, max.results = max.results)
6. └─private$searchByMass(...)
7. └─self$wsGetLiteEntity(...)
8. └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─conn$annotateMzValues(...)
4. └─self$searchForEntries(fieldsFilter, max.results = max.results)
5. └─private$doSearchForEntries(fields = fields, max.results = max.results)
6. └─private$searchByMass(...)
7. └─self$wsGetLiteEntity(...)
8. └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─conn$annotateMzValues(...)
4. └─self$searchForEntries(fieldsFilter, max.results = max.results)
5. └─private$doSearchForEntries(fields = fields, max.results = max.results)
6. └─private$searchByMass(...)
7. └─self$wsGetLiteEntity(...)
8. └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─conn$annotateMzValues(...)
4. └─self$searchForEntries(fieldsFilter, max.results = max.results)
5. └─private$doSearchForEntries(fields = fields, max.results = max.results)
6. └─private$searchByMass(...)
7. └─self$wsGetLiteEntity(...)
8. └─XML::xmlInternalTreeParse(results, asText = TRUE)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 179 ]
Error: Test failures
Execution halted
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed |