Pierrick Roger
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_21 |
| git_last_commit: b8d718f |
| git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:42 -0400 (Mon, 01 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" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| 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 | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbChebi |
| Version: 1.14.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.14.0.tar.gz |
| StartedAt: 2025-08-29 06:54:53 -0000 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 06:56:47 -0000 (Fri, 29 Aug 2025) |
| EllapsedTime: 114.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 1.179 0.121 6.517
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2025-08-29 06:55:58.583][biodb::testContext]
biodb.INFO [2025-08-29 06:55:58.586][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:55:58.587][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-08-29 06:55:58.588][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:55:58.590][biodb::testContext]
biodb.INFO [2025-08-29 06:55:58.598][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:55:58.601][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 06:55:58.610][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:55:58.612][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 06:55:58.613][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 06:55:58.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.618][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 06:55:58.647][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 06:55:58.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.652][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 06:55:58.654][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 06:55:58.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.659][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 06:55:58.660][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 06:55:58.662][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 06:55:58.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.667][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 06:55:58.668][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 06:55:58.670][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 06:55:58.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.675][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 06:55:58.676][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 06:55:58.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.680][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[2025-08-29 06:55:58.681][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 06:55:58.683][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 06:55:58.684][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 06:55:58.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.689][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 06:55:58.691][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 06:55:58.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.696][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 06:55:58.697][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 06:55:58.699][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 06:55:58.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.704][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:55:58.705][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 06:55:58.707][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 06:55:58.708][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 06:55:58.709][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 06:55:58.711][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 06:55:58.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.716][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 06:55:58.717][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 06:55:58.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.722][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 06:55:58.724][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 06:55:58.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.729][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 06:55:58.730][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 06:55:58.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.736][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 06:55:58.737][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 06:55:58.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.742][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 06:55:58.744][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 06:55:58.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.749][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:55:58.750][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 06:55:58.756][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 06:55:58.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.761][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 06:55:58.762][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 06:55:58.764][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 06:55:58.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:58.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:58.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:58.772][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 06:55:58.822][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.847][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 06:55:58.848][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.850][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:55:58.851][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.863][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.865][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.866][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.868][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:55:58.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:55:58.870][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.872][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 06:55:58.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:55:58.874][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.876][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.877][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:55:58.877][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:55:58.877][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:55:58.877][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:55:58.877][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:55:58.878][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:55:58.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:58.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:58.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:55:58.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:58.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:58.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.887][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.889][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:55:58.890][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:55:58.891][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.892][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.894][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 06:55:58.896][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.898][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:55:58.899][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.900][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:55:58.902][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.903][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.904][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.906][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.907][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:55:58.908][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:55:58.910][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.911][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 06:55:58.912][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:55:58.914][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.915][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.916][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:55:58.916][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:55:58.916][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:55:58.916][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:55:58.916][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:55:58.918][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:55:58.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:58.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:58.921][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:55:58.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:58.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:58.925][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.926][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.928][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:55:58.929][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:55:58.930][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.931][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.933][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 06:55:58.935][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.937][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 06:55:58.938][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.939][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:55:58.940][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.942][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.943][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.944][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.946][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:55:58.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:55:58.948][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.949][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 06:55:58.951][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:55:58.952][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.953][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.955][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:55:58.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:58.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:58.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:55:58.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:58.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:58.963][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.965][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:55:58.967][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:55:58.968][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.970][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.971][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 06:55:58.974][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.975][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:55:58.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.978][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:55:58.979][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.981][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.983][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:55:58.984][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:55:58.985][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:55:58.987][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:58.988][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 06:55:58.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:55:58.991][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.992][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:58.993][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:58.995][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:55:58.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:58.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:58.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:55:59.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:59.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:59.002][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:55:59.003][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:59.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:55:59.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:55:59.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:59.008][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:55:59.014][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:55:59.015][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.057][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[2025-08-29 06:55:59.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.063][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[2025-08-29 06:55:59.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.075][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[2025-08-29 06:55:59.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.092][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[2025-08-29 06:55:59.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.098][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[2025-08-29 06:55:59.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.104][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[2025-08-29 06:55:59.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.116][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[2025-08-29 06:55:59.117][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 06:55:59.123][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 06:55:59.125][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 06:55:59.127][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 06:55:59.129][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:55:59.131][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 06:55:59.133][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 06:55:59.135][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 06:55:59.137][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 06:55:59.139][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 06:55:59.141][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:55:59.143][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 06:55:59.145][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 06:55:59.147][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 06:55:59.148][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 06:55:59.150][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 06:55:59.152][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 06:55:59.154][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 06:55:59.156][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:55:59.158][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 06:55:59.160][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 06:55:59.162][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 06:55:59.164][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 06:55:59.166][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 06:55:59.167][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 06:55:59.169][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 06:55:59.171][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 06:55:59.173][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 06:55:59.175][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 06:55:59.177][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 06:55:59.179][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 06:55:59.181][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 06:55:59.183][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 06:55:59.184][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 06:55:59.186][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 06:55:59.188][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 06:55:59.190][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 06:55:59.192][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 06:55:59.194][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 06:55:59.196][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 06:55:59.198][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 06:55:59.199][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 06:55:59.201][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 06:55:59.203][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 06:55:59.205][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 06:55:59.207][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 06:55:59.209][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 06:55:59.210][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 06:55:59.212][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 06:55:59.222][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 06:55:59.224][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 06:55:59.226][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 06:55:59.228][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 06:55:59.230][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 06:55:59.232][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 06:55:59.234][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 06:55:59.236][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 06:55:59.237][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 06:55:59.239][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 06:55:59.241][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 06:55:59.243][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 06:55:59.245][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 06:55:59.247][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 06:55:59.249][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 06:55:59.251][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 06:55:59.253][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 06:55:59.255][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:55:59.257][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:55:59.259][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 06:55:59.261][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 06:55:59.263][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 06:55:59.265][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 06:55:59.267][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 06:55:59.268][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 06:55:59.270][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 06:55:59.272][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 06:55:59.274][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 06:55:59.276][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 06:55:59.278][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 06:55:59.280][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 06:55:59.282][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 06:55:59.284][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 06:55:59.286][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 06:55:59.295][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 06:55:59.297][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:55:59.301][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:55:59.302][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.305][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.354][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[2025-08-29 06:55:59.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:55:59.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:55:59.455][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 06:55:59.468][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 06:55:59.471][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:59.473][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 06:55:59.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:59.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:55:59.477][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:59.478][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:55:59.479][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:59.480][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 06:55:59.482][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 06:55:59.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:55:59.484][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:59.486][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 06:55:59.487][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 06:55:59.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 06:55:59.490][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 06:55:59.491][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:55:59.491][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:55:59.491][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:55:59.492][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 06:55:59.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:59.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:59.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:55:59.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:55:59.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:55:59.500][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:55:59.501][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:55:59.501][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 06:55:59.502][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:55:59.503][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:55:59.505][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 06:55:59.506][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 06:55:59.506][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 06:55:59.515][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:55:59.517][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:55:59.519][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 06:55:59.521][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:55:59.523][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:55:59.526][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:55:59.557][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 06:55:59.558][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 06:55:59.564][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 06:55:59.569][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 06:55:59.575][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:55:59.576][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:55:59.578][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 06:55:59.580][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 06:55:59.601][biodb::testThat]
biodb.INFO [2025-08-29 06:55:59.602][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-08-29 06:55:59.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:55:59.605][biodb::testThat]
biodb.TRACE[2025-08-29 06:55:59.610][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-08-29 06:55:59.613][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:55:59.617][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:55:59.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:55:59.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:55:59.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:55:59.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:55:59.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:55:59.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:55:59.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:55:59.661][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.665][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.690][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:55:59.691][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:55:59.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.693][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.733][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:55:59.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:55:59.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.739][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:55:59.741][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:55:59.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.743][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:55:59.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:55:59.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.751][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:55:59.752][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:55:59.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.755][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:55:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:55:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.762][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:55:59.763][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:55:59.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:55:59.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:55:59.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.773][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:55:59.774][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:55:59.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.777][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.779][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:55:59.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:55:59.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.784][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:55:59.786][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:55:59.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.788][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.790][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:55:59.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:55:59.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.795][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:55:59.797][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:55:59.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.799][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:55:59.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:55:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.807][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:55:59.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:55:59.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.811][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:55:59.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:55:59.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.818][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:55:59.820][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:55:59.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.822][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.824][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:55:59.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:55:59.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.830][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:55:59.832][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:55:59.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.834][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.836][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:55:59.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:55:59.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:55:59.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:55:59.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:55:59.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:55:59.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:55:59.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:55:59.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:55:59.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:55:59.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:55:59.976][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-08-29 06:55:59.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:55:59.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:55:59.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:55:59.984][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:55:59.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:55:59.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:55:59.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.045][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 06:56:00.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 06:56:00.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 06:56:00.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 06:56:00.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.057][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 06:56:00.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 06:56:00.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.063][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 06:56:00.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 06:56:00.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.199][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.204][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.238][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.242][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:00.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.284][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.286][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.289][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.311][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.317][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.322][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.323][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.326][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.327][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.358][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.359][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.362][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.394][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.396][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.398][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.415][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.420][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.425][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.430][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.432][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.434][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.435][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.451][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.456][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.462][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.467][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.468][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.471][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.472][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.487][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.493][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.504][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.505][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.507][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.524][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:00.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:00.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:00.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:00.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:00.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:00.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.540][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:00.541][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:00.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.543][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.545][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:00.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:00.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.576][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.584][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.587][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.620][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.621][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.624][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.640][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.645][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.651][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.652][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.655][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.661][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.663][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.665][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.671][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.673][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.675][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.681][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.683][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.686][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.692][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.693][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.696][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.702][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.704][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.706][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.714][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.716][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.723][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.727][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.733][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.737][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.743][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:00.745][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:00.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.747][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:00.758][biodb::testThat]
biodb.INFO [2025-08-29 06:56:00.759][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-29 06:56:00.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:00.762][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:00.782][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-08-29 06:56:00.791][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:00.797][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-08-29 06:56:00.798][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:00.800][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-08-29 06:56:00.801][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:00.836][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:00.838][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:00.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:00.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:00.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:00.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:00.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:00.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:00.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:00.855][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.857][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.859][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:00.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:00.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.900][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.901][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.904][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.906][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.911][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.917][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:00.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:00.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.922][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.923][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.926][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:00.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:00.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.937][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:00.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.944][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.945][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.948][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.950][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:00.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.955][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:00.957][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.960][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.962][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:00.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:00.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.969][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.972][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:00.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.979][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.981][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:00.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:00.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.991][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:00.992][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:00.995][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:00.996][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:00.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:00.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.002][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:01.004][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:01.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.006][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.008][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:01.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:01.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:01.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:01.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:01.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:01.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:01.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:01.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:01.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:01.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:01.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:01.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:01.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:01.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:01.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:01.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:01.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:01.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:01.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:01.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:01.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:01.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:01.066][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-08-29 06:56:01.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-29 06:56:01.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-29 06:56:01.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-29 06:56:01.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-29 06:56:01.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-29 06:56:01.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-29 06:56:01.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:01.092][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.093][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-29 06:56:01.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:01.095][biodb::testThat]
biodb.TRACE[2025-08-29 06:56:01.099][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:01.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:01.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.103][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:01.105][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-08-29 06:56:01.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:01.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:01.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:01.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:01.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:01.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:01.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:01.160][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-08-29 06:56:01.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 06:56:01.205][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:01.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 06:56:01.231][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:01.233][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 06:56:01.268][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:01.272][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:01.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:01.276][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:01.278][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 06:56:01.281][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-08-29 06:56:01.297][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:01.298][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:01.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.301][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.302][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.304][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.306][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:01.312][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.313][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-08-29 06:56:01.314][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:01.316][biodb::testThat]
biodb.TRACE[2025-08-29 06:56:01.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:01.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:01.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:01.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:01.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:01.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:01.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:01.444][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:01.449][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:01.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:01.452][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:01.454][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-08-29 06:56:01.475][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.476][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-08-29 06:56:01.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:01.479][biodb::testThat]
biodb.TRACE[2025-08-29 06:56:01.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:01.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:01.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:01.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:01.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.559][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 06:56:01.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 06:56:01.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.564][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 06:56:01.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 06:56:01.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:01.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:01.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:01.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:01.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:01.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:01.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.626][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 06:56:01.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.637][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 06:56:01.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 06:56:01.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:01.642][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 06:56:01.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 06:56:01.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:01.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:01.654][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.655][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-29 06:56:01.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:01.658][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.668][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.670][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-29 06:56:01.671][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:01.672][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.683][biodb::testThat]
biodb.INFO [2025-08-29 06:56:01.685][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-29 06:56:01.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:01.687][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:01.692][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-08-29 06:56:04.250][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-08-29 06:56:06.646][biodb::testThat]
biodb.INFO [2025-08-29 06:56:06.647][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-29 06:56:06.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:06.650][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:07.327][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-08-29 06:56:09.052][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:09.054][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:09.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.057][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.059][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:09.060][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:09.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.063][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:09.066][biodb::testThat]
biodb.INFO [2025-08-29 06:56:09.067][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-08-29 06:56:09.069][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:09.070][biodb::testThat]
biodb.TRACE[2025-08-29 06:56:09.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:09.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:09.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:09.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:09.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:09.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:09.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:09.217][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:09.222][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:09.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:09.226][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:09.228][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 06:56:09.346][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:09.351][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:09.353][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:09.354][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:09.356][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-08-29 06:56:09.374][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 06:56:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 06:56:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:09.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:09.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:09.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:09.421][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:09.426][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:09.428][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 06:56:09.429][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:09.432][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 06:56:09.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:09.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:09.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:09.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:09.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:09.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:09.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:09.449][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-08-29 06:56:09.525][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:09.527][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-08-29 06:56:09.529][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 06:56:09.530][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 06:56:09.532][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:09.533][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:56:09.534][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 06:56:09.536][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 06:56:09.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:09.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:09.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:09.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:09.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:09.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:09.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:09.553][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-08-29 06:56:09.557][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 06:56:09.559][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 06:56:09.560][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-08-29 06:56:13.278][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-08-29 06:56:16.998][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 06:56:17.001][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-08-29 06:56:17.022][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-08-29 06:56:17.026][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-08-29 06:56:17.028][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 06:56:17.029][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:17.031][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:17.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:17.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:17.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:17.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:17.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:17.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:17.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:17.049][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.051][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.054][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.061][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:17.062][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:17.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.065][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.067][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:17.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:17.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.072][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:17.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:17.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.076][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.079][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:17.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:17.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.084][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:17.086][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:17.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:17.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:17.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.103][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:17.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:17.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.108][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:17.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:17.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.116][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:17.118][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:17.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.121][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.123][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:17.124][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.127][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.129][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:17.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.135][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:17.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:17.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.140][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:17.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:17.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.148][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:17.150][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:17.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.153][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:17.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:17.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.161][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:17.163][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:17.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.166][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.168][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:17.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:17.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.174][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:17.176][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:17.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.179][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:17.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:17.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:17.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:17.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:17.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:17.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:17.272][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-08-29 06:56:17.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:17.307][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:17.312][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:17.315][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 06:56:17.316][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:17.319][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 06:56:17.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:17.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:17.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:17.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:17.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:17.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:17.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:17.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:17.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:17.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:17.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:17.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:17.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:17.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:17.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:17.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:17.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:17.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:17.394][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-08-29 06:56:17.396][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:17.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-08-29 06:56:17.400][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 06:56:17.401][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 06:56:17.403][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:17.404][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:56:17.406][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 06:56:17.407][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 06:56:17.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:17.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:17.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:17.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:17.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:17.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:17.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:17.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-08-29 06:56:17.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 06:56:17.469][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 06:56:17.501][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-08-29 06:56:18.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-08-29 06:56:19.273][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 06:56:19.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-08-29 06:56:19.280][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-08-29 06:56:19.284][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-08-29 06:56:19.286][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 06:56:19.288][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:19.289][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:19.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:19.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:19.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:19.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:19.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:19.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:19.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:19.308][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.312][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.319][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:19.321][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:19.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.323][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.325][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:19.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.331][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:19.332][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:19.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.335][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:19.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:19.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.343][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:19.344][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:19.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.347][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:19.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:19.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.354][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:19.356][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:19.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.358][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:19.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:19.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.366][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:19.367][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:19.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.370][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.371][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:19.373][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.376][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.377][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:19.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.383][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:19.385][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:19.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.387][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:19.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.395][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:19.396][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:19.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.399][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:19.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:19.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.407][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:19.408][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:19.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.411][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.412][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:19.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:19.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.418][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:19.420][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:19.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.422][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.424][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:19.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:19.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:19.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:19.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:19.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:19.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:19.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:19.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:19.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:19.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:19.486][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-08-29 06:56:19.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:19.538][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:19.543][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:19.545][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:19.547][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:19.548][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 06:56:19.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:19.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:19.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:19.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:19.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:19.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:19.565][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.TRACE[2025-08-29 06:56:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:19.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:19.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:19.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:19.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:19.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:19.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:19.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:19.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:19.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:19.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:19.597][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-08-29 06:56:19.598][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:19.600][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-08-29 06:56:19.602][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 06:56:19.604][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 06:56:19.605][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:19.607][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:56:19.608][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 06:56:19.609][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 06:56:19.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:19.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:19.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:19.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:19.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:19.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:19.626][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[2025-08-29 06:56:19.627][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-08-29 06:56:19.631][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 06:56:19.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 06:56:19.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-08-29 06:56:21.566][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-08-29 06:56:25.731][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 06:56:25.734][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-08-29 06:56:25.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-08-29 06:56:25.743][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-08-29 06:56:25.745][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 06:56:25.747][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:25.749][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:25.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:25.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:25.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:25.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:25.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:25.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:25.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:25.768][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.773][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.782][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:25.784][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:25.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.788][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:25.790][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:25.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.793][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.794][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:25.796][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:25.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.799][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.800][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:25.802][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:25.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.805][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.806][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:25.808][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:25.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.810][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.812][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:25.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.816][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:25.820][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:25.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.822][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.824][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:25.825][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:25.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.828][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:25.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:25.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.836][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:25.837][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:25.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.840][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:25.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:25.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.847][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:25.849][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:25.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.852][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:25.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:25.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:25.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:25.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:25.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:25.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:25.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:25.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:25.922][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-08-29 06:56:25.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:25.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:25.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:25.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:25.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:25.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:25.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:25.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:25.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:25.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:25.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:25.965][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-08-29 06:56:25.967][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:25.969][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-08-29 06:56:25.971][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 06:56:25.972][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 06:56:25.974][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:25.975][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:56:25.977][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 06:56:25.978][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 06:56:25.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:25.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:25.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:25.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:25.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:25.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:25.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:25.997][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-08-29 06:56:26.000][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 06:56:26.002][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 06:56:26.004][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-08-29 06:56:26.706][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-08-29 06:56:28.436][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 06:56:28.443][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-08-29 06:56:28.451][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-08-29 06:56:28.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-08-29 06:56:28.459][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 06:56:28.462][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:28.465][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:28.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:28.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:28.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:28.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:28.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:28.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:28.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:28.499][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.501][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.504][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.513][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:28.514][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:28.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.517][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.519][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:28.521][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:28.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.524][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.526][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:28.528][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:28.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.530][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.532][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:28.534][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:28.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.537][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.539][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:28.541][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:28.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.544][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.546][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:28.548][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.551][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.553][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:28.554][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:28.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.557][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.559][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:28.561][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:28.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.564][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:28.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:28.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.573][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:28.575][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:28.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.578][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.580][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:28.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:28.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.586][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:28.588][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:28.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.591][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:28.677][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-08-29 06:56:28.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:28.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:28.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:28.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:28.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:28.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:28.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:28.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:28.725][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-08-29 06:56:28.727][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:28.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-08-29 06:56:28.732][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:28.735][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml".
biodb.DEBUG[2025-08-29 06:56:28.737][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:28.739][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:28.741][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:28.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:28.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:28.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:28.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:28.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:28.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:28.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:28.763][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.765][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.768][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.777][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:28.779][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:28.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.782][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.784][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:28.786][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:28.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.789][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.791][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:28.793][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:28.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.796][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.798][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:28.800][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:28.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.803][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.805][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:28.807][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:28.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.810][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.812][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:28.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.816][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:28.820][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:28.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.823][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.825][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:28.827][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:28.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.830][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:28.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:28.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.839][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:28.841][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:28.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.844][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.846][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:28.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:28.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.853][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:28.855][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:28.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.858][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:28.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:28.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:28.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:28.938][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-08-29 06:56:28.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:28.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:28.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:28.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:28.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:28.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:28.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:28.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:28.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:28.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:28.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:28.983][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-08-29 06:56:28.984][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:28.987][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-08-29 06:56:28.989][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:28.992][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml".
biodb.DEBUG[2025-08-29 06:56:28.993][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:28.995][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:28.997][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:28.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:29.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:29.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:29.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:29.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:29.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:29.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:29.015][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.017][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.027][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.028][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.031][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.033][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.038][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.039][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.042][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.050][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.052][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.054][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.064][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.067][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.075][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.077][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.080][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.088][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.092][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.101][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.103][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.111][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.113][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.115][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.124][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:29.125][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:29.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.128][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.130][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:29.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:29.139][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:29.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:29.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:29.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:29.215][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-08-29 06:56:29.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:29.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:29.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:29.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:29.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:29.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:29.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:29.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:29.248][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-08-29 06:56:29.250][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:29.252][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-08-29 06:56:29.254][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:29.256][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml".
biodb.DEBUG[2025-08-29 06:56:29.258][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:29.260][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:29.261][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:29.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:29.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:29.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:29.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:29.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:29.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:29.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:29.281][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.283][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.285][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.293][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.295][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.297][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.299][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.305][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.309][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.311][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.317][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.318][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.321][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.328][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.330][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.333][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.341][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.342][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.345][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.347][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.353][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.355][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.358][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.360][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.366][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.368][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.371][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.380][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.382][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.384][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.392][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:29.394][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:29.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.396][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.398][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:29.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:29.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.404][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:29.405][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:29.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.408][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.410][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:29.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:29.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:29.488][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-08-29 06:56:29.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:29.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:29.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:29.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:29.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:29.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:29.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:29.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:29.524][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-08-29 06:56:29.525][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:29.527][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-08-29 06:56:29.540][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:29.545][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml".
biodb.DEBUG[2025-08-29 06:56:29.548][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:29.551][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:29.554][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:29.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:29.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:29.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:29.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:29.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:29.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:29.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:29.586][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.588][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.591][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.600][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.601][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.604][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.614][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.615][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.619][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.621][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.629][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.631][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.634][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.644][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.646][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.650][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.661][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.663][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.667][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.670][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.672][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.677][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.679][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.689][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.691][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.695][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.704][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.708][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.717][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:29.719][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:29.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.722][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.724][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:29.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:29.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.731][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:29.733][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:29.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.736][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.738][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:29.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:29.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:29.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:29.826][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-08-29 06:56:29.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:29.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:29.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:29.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:29.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:29.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:29.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:29.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:29.862][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-08-29 06:56:29.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:29.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-08-29 06:56:29.869][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:29.871][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml".
biodb.DEBUG[2025-08-29 06:56:29.873][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:29.875][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:29.877][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:29.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:29.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:29.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:29.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:29.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:29.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:29.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:29.896][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.897][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.900][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:29.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:29.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.907][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.909][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.911][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.913][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:29.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:29.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.919][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.920][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.923][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:29.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:29.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.931][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.932][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.935][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:29.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:29.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.942][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.944][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.947][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:29.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.956][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:29.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.959][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.961][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.962][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.965][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.967][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:29.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:29.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.973][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.978][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:29.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.986][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.988][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.991][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:29.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:29.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:29.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:29.999][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.000][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.003][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.005][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.011][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.012][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.015][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.017][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.080][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-08-29 06:56:30.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:30.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:30.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:30.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:30.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:30.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:30.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:30.122][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-08-29 06:56:30.124][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:30.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-08-29 06:56:30.128][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:30.131][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml".
biodb.DEBUG[2025-08-29 06:56:30.133][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:30.134][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:30.136][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:30.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:30.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:30.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:30.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:30.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:30.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:30.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:30.157][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.162][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.170][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:30.171][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:30.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.174][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.176][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:30.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:30.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.182][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:30.183][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:30.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.186][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:30.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:30.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.194][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:30.195][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:30.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.198][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:30.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:30.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.206][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.208][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.211][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.219][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:30.221][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:30.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.224][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.226][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:30.227][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.230][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.232][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:30.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.238][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.239][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.242][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.250][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:30.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:30.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.254][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:30.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:30.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.262][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.264][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.266][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.268][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.274][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.276][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.350][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-08-29 06:56:30.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:30.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:30.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:30.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:30.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:30.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:30.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:30.394][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-08-29 06:56:30.395][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:30.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-08-29 06:56:30.399][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:30.402][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml".
biodb.DEBUG[2025-08-29 06:56:30.404][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:30.405][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:30.407][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:30.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:30.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:30.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:30.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:30.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:30.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:30.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:30.426][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.431][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.439][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:30.441][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:30.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.444][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.446][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:30.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:30.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.453][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:30.454][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:30.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.457][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:30.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:30.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.465][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:30.467][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:30.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.470][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:30.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:30.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.478][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.479][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.482][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.491][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:30.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:30.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.496][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.498][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:30.499][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.502][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.504][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:30.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.512][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.515][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.523][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:30.525][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:30.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.528][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:30.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:30.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.536][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.538][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.541][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.542][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.549][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.550][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.553][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.555][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.621][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-08-29 06:56:30.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:30.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:30.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:30.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:30.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:30.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:30.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:30.665][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-08-29 06:56:30.667][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:30.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-08-29 06:56:30.672][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:30.675][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml".
biodb.DEBUG[2025-08-29 06:56:30.677][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:30.678][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:30.680][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:30.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:30.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:30.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:30.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:30.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:30.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:30.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:30.699][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.701][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.704][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.711][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:30.713][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:30.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.716][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.718][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:30.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:30.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.724][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:30.725][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:30.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.728][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:30.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:30.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.736][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:30.737][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:30.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.740][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:30.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:30.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.748][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.753][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:30.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.761][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:30.763][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:30.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.768][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:30.769][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.772][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.774][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:30.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.781][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.782][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.785][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:30.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.794][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:30.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:30.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.799][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:30.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:30.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.807][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.809][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.812][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.813][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:30.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:30.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.819][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.821][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.823][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.825][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:30.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:30.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:30.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:30.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:30.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.887][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-08-29 06:56:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:30.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:30.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:30.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:30.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:30.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:30.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:30.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:30.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:30.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:30.982][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-08-29 06:56:30.984][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:30.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-08-29 06:56:30.990][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:30.993][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2025-08-29 06:56:30.995][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:30.998][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:31.000][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:31.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:31.026][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.028][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.031][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.040][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.041][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.044][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.046][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.053][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.054][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.057][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.065][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:31.067][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:31.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.070][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.072][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.074][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.077][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.079][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.080][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.083][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.085][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.087][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.090][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.091][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.098][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.099][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.102][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.111][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.113][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.116][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.126][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.130][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.138][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:31.140][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:31.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.143][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.208][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-08-29 06:56:31.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:31.241][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-08-29 06:56:31.243][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:31.245][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-08-29 06:56:31.247][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:31.249][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2025-08-29 06:56:31.251][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:31.253][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:31.254][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:31.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:31.286][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.288][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.290][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.298][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.299][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.302][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.304][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.309][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.311][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.313][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.321][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:31.322][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:31.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.325][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.331][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.332][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.334][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.336][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.338][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.339][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.342][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.344][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.349][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.351][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.353][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.361][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.362][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.365][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.372][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.374][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.376][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.378][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.383][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:31.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:31.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.387][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.443][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-08-29 06:56:31.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:31.476][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-08-29 06:56:31.477][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:31.479][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-08-29 06:56:31.481][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:31.484][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2025-08-29 06:56:31.485][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:31.487][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:31.488][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:31.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:31.506][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.508][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.518][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.522][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.529][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.530][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.541][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.550][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:31.551][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:31.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.554][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:31.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:31.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.561][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.562][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.565][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.573][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.577][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.579][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.580][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.583][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.584][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.590][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.592][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.594][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.602][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.603][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.606][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.614][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.615][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.618][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.619][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.625][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:31.626][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:31.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.629][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.631][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:31.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:31.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.694][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-08-29 06:56:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:31.727][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-08-29 06:56:31.728][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:31.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-08-29 06:56:31.732][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:31.735][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2025-08-29 06:56:31.736][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:31.738][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:31.740][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:31.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:31.758][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.759][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.762][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.769][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.770][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.773][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.775][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:31.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:31.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.780][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.782][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.784][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:31.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:31.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:31.793][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:31.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.803][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:31.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:31.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.811][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.812][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.815][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:31.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.822][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.824][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:31.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.826][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.828][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.830][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.832][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.834][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:31.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.840][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.841][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.844][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:31.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.851][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.853][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.856][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:31.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:31.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.863][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.865][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.867][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.869][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:31.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:31.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.875][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:31.876][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:31.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.879][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.881][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:31.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:31.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:31.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:31.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:31.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.942][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-08-29 06:56:31.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:31.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:31.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:31.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:31.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:31.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:31.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:31.974][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-08-29 06:56:31.975][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:31.978][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-08-29 06:56:31.979][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:31.982][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2025-08-29 06:56:31.983][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:31.985][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:31.986][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:31.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:31.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:31.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:31.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:31.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:32.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:32.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:32.004][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.008][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.015][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.017][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.021][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.027][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.028][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.031][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.038][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.039][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.042][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.049][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.051][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.061][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.071][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.073][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.075][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.076][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.079][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.081][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.086][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.088][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.090][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.098][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.099][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.102][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.109][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.111][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.113][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.115][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.121][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.123][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.126][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:32.191][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-08-29 06:56:32.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:32.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:32.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:32.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:32.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:32.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:32.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:32.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:32.224][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-08-29 06:56:32.225][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:32.227][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-08-29 06:56:32.229][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:32.232][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2025-08-29 06:56:32.233][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:32.235][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:32.236][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:32.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:32.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:32.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:32.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:32.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:32.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:32.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:32.255][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.256][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.259][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.266][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.268][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.270][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.272][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.278][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.279][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.282][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.291][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.293][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.300][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.302][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.304][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.323][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.326][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.330][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.332][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.338][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.339][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.342][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.350][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.354][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.362][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.364][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.367][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.369][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.375][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.376][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.379][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.381][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:32.443][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-08-29 06:56:32.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:32.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:32.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:32.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:32.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:32.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:32.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:32.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:32.476][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-08-29 06:56:32.477][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:32.479][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-08-29 06:56:32.481][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:32.484][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2025-08-29 06:56:32.485][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:32.487][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:32.489][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:32.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:32.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:32.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:32.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:32.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:32.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:32.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:32.507][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.508][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.518][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.520][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.522][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.524][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.530][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.532][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.534][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.542][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.544][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.546][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.555][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.558][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.566][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.567][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.570][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.572][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.573][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.576][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.578][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.592][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.597][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.604][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.609][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.617][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.618][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.621][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.623][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.629][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.630][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.633][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.635][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:32.698][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-08-29 06:56:32.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:32.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:32.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:32.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:32.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:32.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:32.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:32.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:32.731][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-08-29 06:56:32.733][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:32.735][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-08-29 06:56:32.737][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:32.739][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2025-08-29 06:56:32.741][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:32.743][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:32.745][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:32.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:32.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:32.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:32.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:32.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:32.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:32.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:32.764][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.765][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.768][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.776][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.777][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.780][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.782][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:32.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:32.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.788][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.792][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.794][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:32.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:32.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.800][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.801][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.804][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:32.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:32.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.819][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.821][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.823][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:32.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.832][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.833][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:32.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.836][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.838][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.840][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.843][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.845][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:32.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.856][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:32.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.882][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.887][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:32.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:32.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.895][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.897][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.900][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:32.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:32.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.908][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.910][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.913][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.914][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:32.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:32.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:32.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:32.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:32.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:32.981][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-08-29 06:56:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:32.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:32.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:32.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:33.016][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-08-29 06:56:33.018][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:33.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-08-29 06:56:33.022][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:33.025][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2025-08-29 06:56:33.026][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:33.028][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:33.030][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:33.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.049][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.051][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.053][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.061][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:33.063][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:33.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.065][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.067][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:33.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:33.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.074][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:33.075][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:33.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.078][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.080][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:33.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:33.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.086][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:33.088][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:33.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.091][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:33.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:33.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:33.100][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:33.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.103][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:33.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:33.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.110][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:33.111][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:33.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.116][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:33.117][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.120][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.121][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:33.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.127][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:33.129][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:33.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.131][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:33.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:33.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.139][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:33.140][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:33.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.143][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:33.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:33.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.159][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:33.161][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:33.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.163][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:33.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:33.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:33.173][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:33.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.175][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.177][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:33.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:33.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:33.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:33.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:33.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:33.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:33.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:33.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:33.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:33.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.240][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-08-29 06:56:33.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:33.287][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:33.289][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:33.291][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:33.293][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 06:56:33.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.310][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.TRACE[2025-08-29 06:56:33.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.539][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.TRACE[2025-08-29 06:56:33.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.571][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.TRACE[2025-08-29 06:56:33.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.865][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.TRACE[2025-08-29 06:56:33.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.930][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[2025-08-29 06:56:33.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:33.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:33.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:33.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:33.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:33.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:33.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:33.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:33.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:33.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:33.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.073][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:34.078][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:34.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2025-08-29 06:56:34.081][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:34.084][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2025-08-29 06:56:34.088][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:34.092][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:34.094][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2025-08-29 06:56:34.096][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:34.098][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2025-08-29 06:56:34.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.114][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[2025-08-29 06:56:34.116][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-08-29 06:56:34.117][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:34.119][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-08-29 06:56:34.121][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:34.124][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2025-08-29 06:56:34.125][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:34.127][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:34.129][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:34.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.147][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.149][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.152][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.160][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:34.161][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:34.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.164][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.166][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:34.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:34.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.172][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:34.174][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:34.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.176][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:34.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:34.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.184][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:34.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:34.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.189][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:34.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:34.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.197][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.205][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.209][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.217][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:34.218][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:34.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.223][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:34.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:34.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.229][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:34.230][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:34.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.233][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.235][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:34.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:34.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.241][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.245][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.253][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:34.254][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:34.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.257][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:34.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:34.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:34.267][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:34.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.269][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:34.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:34.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.277][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:34.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:34.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.281][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:34.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:34.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.346][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-08-29 06:56:34.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:34.412][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-08-29 06:56:34.413][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:34.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-08-29 06:56:34.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:34.420][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2025-08-29 06:56:34.421][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:34.423][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:34.425][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:34.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.443][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.455][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:34.457][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:34.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.459][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.461][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:34.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:34.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.475][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:34.477][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:34.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.480][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:34.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:34.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.487][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:34.489][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:34.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.492][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:34.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:34.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.501][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.503][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:34.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.511][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:34.513][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:34.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.515][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.517][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:34.518][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:34.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.521][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.523][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:34.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:34.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.529][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.530][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.533][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.541][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:34.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:34.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.545][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:34.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:34.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.553][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:34.554][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:34.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.557][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:34.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:34.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.565][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:34.566][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:34.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.569][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:34.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:34.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:34.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:34.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.633][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-08-29 06:56:34.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.677][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:34.681][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:34.683][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:34.685][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:34.687][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 06:56:34.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.787][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.TRACE[2025-08-29 06:56:34.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.903][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.TRACE[2025-08-29 06:56:34.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.934][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.TRACE[2025-08-29 06:56:34.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:34.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:34.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:34.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:34.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:34.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:34.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:34.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:34.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:34.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:34.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:34.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.037][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.TRACE[2025-08-29 06:56:35.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.331][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.TRACE[2025-08-29 06:56:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:35.451][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:35.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 06:56:35.455][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:35.457][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 06:56:35.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.602][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.TRACE[2025-08-29 06:56:35.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.738][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.TRACE[2025-08-29 06:56:35.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.800][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.TRACE[2025-08-29 06:56:35.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.873][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.TRACE[2025-08-29 06:56:35.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.937][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.TRACE[2025-08-29 06:56:35.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:35.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:35.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:35.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:35.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:35.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:35.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:35.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:35.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:35.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:35.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.034][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[2025-08-29 06:56:36.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:36.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:36.195][biodb::testThat]
biodb.INFO [2025-08-29 06:56:36.196][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-29 06:56:36.198][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:36.199][biodb::testThat]
biodb.TRACE[2025-08-29 06:56:36.203][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 06:56:36.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 06:56:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:36.253][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:36.257][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:36.259][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 06:56:36.261][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:36.263][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 06:56:36.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.298][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:36.303][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:36.304][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 06:56:36.306][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:36.308][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 06:56:36.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:36.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.383][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 06:56:36.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.410][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.411][private$selectFields]
biodb.TRACE[2025-08-29 06:56:36.413][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:36.414][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:36.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.417][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.422][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.423][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.425][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.428][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.429][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.431][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.432][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.434][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.437][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.439][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:36.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.472][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 06:56:36.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.499][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.500][private$selectFields]
biodb.TRACE[2025-08-29 06:56:36.502][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:36.503][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:36.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.511][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.516][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.517][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.519][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.521][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.524][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.526][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:36.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.545][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 06:56:36.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.572][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.574][private$selectFields]
biodb.TRACE[2025-08-29 06:56:36.575][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:36.576][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:36.578][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.579][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.581][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.583][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.586][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.589][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.590][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.591][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.593][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.594][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.597][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.598][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:36.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.631][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 06:56:36.632][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 06:56:36.634][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 06:56:36.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.762][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[2025-08-29 06:56:36.766][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:36.770][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:36.772][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-29 06:56:36.774][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:36.777][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-29 06:56:36.781][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:36.785][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:36.787][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-29 06:56:36.789][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:36.791][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-29 06:56:36.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:36.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:36.933][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 06:56:36.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:36.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:36.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:36.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:36.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:36.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:36.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:36.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:36.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:36.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:36.995][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:36.996][private$selectFields]
biodb.TRACE[2025-08-29 06:56:36.997][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:36.999][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.000][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.001][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.003][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.006][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.007][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.009][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.011][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.014][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.016][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.020][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.021][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:37.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.040][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 06:56:37.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.125][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.127][private$selectFields]
biodb.TRACE[2025-08-29 06:56:37.128][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:37.129][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.134][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.136][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.137][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.139][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.158][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.161][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.163][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.165][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:37.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.182][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 06:56:37.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.209][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.210][private$selectFields]
biodb.TRACE[2025-08-29 06:56:37.211][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:37.212][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.214][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.216][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.219][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.220][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.224][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.226][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.227][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.232][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.234][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:37.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.252][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 06:56:37.254][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 06:56:37.255][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 06:56:37.266][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:37.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:37.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:37.276][biodb::testThat]
biodb.INFO [2025-08-29 06:56:37.278][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-29 06:56:37.279][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:37.280][biodb::testThat]
biodb.TRACE[2025-08-29 06:56:37.284][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 06:56:37.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 06:56:37.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:37.332][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:37.344][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:37.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 06:56:37.348][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:37.350][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 06:56:37.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.386][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:37.390][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:37.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 06:56:37.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:37.396][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 06:56:37.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:37.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.461][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 06:56:37.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.492][private$selectFields]
biodb.TRACE[2025-08-29 06:56:37.493][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:37.495][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.496][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.497][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.501][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.507][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.508][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.510][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.511][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.515][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.517][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:37.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.535][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 06:56:37.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.564][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.565][private$selectFields]
biodb.TRACE[2025-08-29 06:56:37.567][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:37.568][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.569][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.572][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.575][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.578][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.581][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.582][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.584][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.587][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.590][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.592][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:37.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.619][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 06:56:37.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.646][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.647][private$selectFields]
biodb.TRACE[2025-08-29 06:56:37.649][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:37.650][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.651][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.653][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.654][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.657][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.658][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.659][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.662][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.665][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.666][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.667][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.670][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.671][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:37.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.689][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 06:56:37.691][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 06:56:37.692][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 06:56:37.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:37.744][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:37.748][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:37.750][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-29 06:56:37.752][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:37.754][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-29 06:56:37.758][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:37.763][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:37.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-29 06:56:37.766][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:37.768][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-29 06:56:37.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.784][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.TRACE[2025-08-29 06:56:37.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:37.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:37.875][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 06:56:37.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.903][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.905][private$selectFields]
biodb.TRACE[2025-08-29 06:56:37.906][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:37.907][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.914][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.917][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.920][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.921][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.923][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.926][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.928][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.930][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:37.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.949][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 06:56:37.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:37.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:37.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:37.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:37.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:37.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:37.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:37.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.979][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.980][private$selectFields]
biodb.TRACE[2025-08-29 06:56:37.981][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:37.983][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:37.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.986][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.987][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.990][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.991][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.993][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:37.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:37.996][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:37.997][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:37.999][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.002][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.005][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.006][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.025][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 06:56:38.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.054][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.055][private$selectFields]
biodb.TRACE[2025-08-29 06:56:38.057][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:38.058][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:38.060][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.066][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.067][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.072][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.073][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.075][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.076][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.078][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.081][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.083][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.104][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 06:56:38.105][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 06:56:38.107][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 06:56:38.126][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:38.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:38.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:38.138][biodb::testThat]
biodb.INFO [2025-08-29 06:56:38.139][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-29 06:56:38.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:38.142][biodb::testThat]
biodb.TRACE[2025-08-29 06:56:38.146][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 06:56:38.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 06:56:38.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:38.217][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:38.223][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:38.226][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 06:56:38.228][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:38.231][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 06:56:38.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.270][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:38.275][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:38.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 06:56:38.279][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:38.281][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 06:56:38.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:38.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.352][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 06:56:38.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.368][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.TRACE[2025-08-29 06:56:38.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.381][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.382][private$selectFields]
biodb.TRACE[2025-08-29 06:56:38.384][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:38.385][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:38.387][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.392][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.394][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.398][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.400][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.401][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.403][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.404][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.407][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.409][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.443][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 06:56:38.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.471][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.472][private$selectFields]
biodb.TRACE[2025-08-29 06:56:38.474][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:38.475][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:38.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.478][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.479][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.482][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.483][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.485][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.487][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.489][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.490][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.491][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.496][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.497][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.516][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 06:56:38.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.530][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.TRACE[2025-08-29 06:56:38.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.543][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.544][private$selectFields]
biodb.TRACE[2025-08-29 06:56:38.545][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:38.547][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:38.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.549][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.551][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.554][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.555][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.557][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.559][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.561][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.562][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.568][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.569][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.588][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 06:56:38.589][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 06:56:38.591][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 06:56:38.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:38.660][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:38.665][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:38.667][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-29 06:56:38.668][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:38.670][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-29 06:56:38.674][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:38.679][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:38.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-29 06:56:38.691][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:38.693][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-29 06:56:38.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:38.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:38.792][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 06:56:38.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.820][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.821][private$selectFields]
biodb.TRACE[2025-08-29 06:56:38.822][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:38.823][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:38.825][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.826][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.828][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.830][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.836][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.839][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.840][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.842][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.844][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.846][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.865][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 06:56:38.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.892][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.893][private$selectFields]
biodb.TRACE[2025-08-29 06:56:38.894][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:38.896][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:38.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.898][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.900][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.902][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.905][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.908][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.910][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.913][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.916][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.917][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.943][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 06:56:38.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:38.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:38.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:38.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:38.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:38.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:38.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:38.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.971][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.973][private$selectFields]
biodb.TRACE[2025-08-29 06:56:38.974][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 06:56:38.975][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 06:56:38.977][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.978][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.982][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.984][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.985][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.988][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.989][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.991][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 06:56:38.992][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.994][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:38.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:38.997][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:38.998][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 06:56:38.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.017][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 06:56:39.019][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 06:56:39.020][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 06:56:39.046][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:39.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 06:56:39.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:39.056][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.058][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-08-29 06:56:39.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:39.060][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:39.063][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-08-29 06:56:39.064][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:39.066][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-08-29 06:56:39.068][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:39.070][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2025-08-29 06:56:39.072][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:39.074][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:39.075][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:39.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:39.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:39.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:39.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:39.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:39.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:39.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:39.093][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.097][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.105][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:39.106][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:39.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.109][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.110][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:39.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:39.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.116][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:39.118][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:39.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.120][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.122][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.124][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.126][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.128][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.129][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.132][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.134][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:39.135][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:39.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.138][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.144][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.146][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:39.147][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:39.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.150][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.152][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:39.154][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:39.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.156][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.158][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:39.159][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:39.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.162][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:39.229][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-08-29 06:56:39.230][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-08-29 06:56:39.241][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.242][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-08-29 06:56:39.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:39.245][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:39.259][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-08-29 06:56:39.260][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-08-29 06:56:39.262][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-08-29 06:56:39.264][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-08-29 06:56:39.266][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-08-29 06:56:39.270][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2025-08-29 06:56:39.272][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:39.273][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-08-29 06:56:39.275][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:39.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:39.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:39.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:39.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:39.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:39.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:39.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:39.293][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.295][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.297][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.305][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:39.306][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:39.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.309][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.311][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:39.312][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:39.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.315][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.317][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:39.319][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:39.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.321][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.323][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.324][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.327][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.329][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.330][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.333][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.335][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:39.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:39.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.339][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.345][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.347][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:39.348][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:39.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.351][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.353][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:39.354][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:39.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.357][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.359][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:39.360][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:39.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.363][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:39.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:39.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:39.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:39.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:39.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:39.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:39.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:39.420][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.422][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.424][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.432][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:39.433][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:39.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.436][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:39.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:39.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.444][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:39.445][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:39.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:39.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:39.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.465][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:39.467][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:39.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.469][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:39.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:39.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.477][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.479][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.482][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.489][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.494][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.495][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.501][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:39.503][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:39.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.505][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.507][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:39.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:39.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.513][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.515][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.517][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.525][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:39.526][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:39.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.529][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:39.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:39.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.537][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:39.538][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:39.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.541][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.543][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:39.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:39.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.549][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:39.550][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:39.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.553][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:39.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:39.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:39.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:39.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:39.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:39.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:39.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:39.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:39.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:39.617][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.619][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.622][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.629][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:39.631][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:39.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.634][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.635][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:39.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:39.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.641][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:39.643][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:39.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.646][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:39.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:39.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.654][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:39.655][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:39.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.658][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:39.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:39.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.666][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.667][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.670][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:39.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.678][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.679][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.682][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:39.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.690][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:39.692][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:39.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.695][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.697][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:39.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:39.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.703][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.704][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.707][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.724][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:39.726][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:39.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.729][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:39.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:39.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.737][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:39.739][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:39.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.742][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:39.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:39.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.750][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:39.751][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:39.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.754][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:39.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:39.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:39.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:39.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:39.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:39.855][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-08-29 06:56:39.857][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-08-29 06:56:39.858][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-08-29 06:56:39.876][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.877][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-08-29 06:56:39.878][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:39.880][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.913][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.914][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-08-29 06:56:39.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:39.917][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.928][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.929][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-08-29 06:56:39.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:39.932][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:39.935][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:39.940][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:39.942][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2025-08-29 06:56:39.944][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:39.946][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2025-08-29 06:56:39.962][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:39.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:39.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.966][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:39.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.969][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:39.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:39.972][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 06:56:39.974][biodb::testThat]
biodb.INFO [2025-08-29 06:56:39.984][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-08-29 06:56:39.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:39.987][biodb::testThat]
biodb.ERROR[2025-08-29 06:56:40.006][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-08-29 06:56:40.027][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-08-29 06:56:40.045][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 06:56:40.046][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 06:56:40.048][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 06:56:40.049][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 06:56:40.050][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.053][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.055][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.057][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.INFO [2025-08-29 06:56:40.070][biodb::testContext]
biodb.INFO [2025-08-29 06:56:40.072][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:56:40.073][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-08-29 06:56:40.074][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:56:40.076][biodb::testContext]
biodb.INFO [2025-08-29 06:56:40.079][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:56:40.081][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 06:56:40.086][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:40.087][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 06:56:40.089][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 06:56:40.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.094][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 06:56:40.095][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 06:56:40.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.101][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 06:56:40.102][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 06:56:40.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.107][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 06:56:40.108][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 06:56:40.110][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 06:56:40.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.114][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[2025-08-29 06:56:40.115][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 06:56:40.116][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 06:56:40.118][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 06:56:40.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.123][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 06:56:40.124][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 06:56:40.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.128][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[2025-08-29 06:56:40.129][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 06:56:40.131][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 06:56:40.132][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 06:56:40.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.137][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 06:56:40.139][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 06:56:40.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.144][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 06:56:40.145][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 06:56:40.147][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 06:56:40.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.152][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:56:40.153][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 06:56:40.155][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 06:56:40.156][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 06:56:40.158][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 06:56:40.159][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 06:56:40.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.164][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 06:56:40.166][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 06:56:40.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.171][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 06:56:40.172][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 06:56:40.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.176][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[2025-08-29 06:56:40.177][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 06:56:40.179][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 06:56:40.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.184][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 06:56:40.185][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 06:56:40.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.190][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 06:56:40.192][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 06:56:40.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.197][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:56:40.198][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 06:56:40.203][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 06:56:40.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.208][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 06:56:40.210][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 06:56:40.211][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 06:56:40.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.217][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 06:56:40.268][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.269][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 06:56:40.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:40.273][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.275][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.276][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.277][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.279][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:56:40.280][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:40.281][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.283][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 06:56:40.284][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:40.285][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.287][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.288][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:40.288][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:40.288][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:40.288][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:56:40.288][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:56:40.289][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:40.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.293][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:40.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.297][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.299][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.300][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:40.301][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:40.302][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.304][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.306][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 06:56:40.308][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.309][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:56:40.311][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.312][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:40.314][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.315][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.316][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.318][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.319][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:56:40.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:40.322][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.323][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 06:56:40.325][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:40.326][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.327][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.329][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:40.329][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:40.329][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:40.329][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:56:40.329][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:56:40.330][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:40.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.334][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:40.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.338][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.340][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.341][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:40.342][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:40.344][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.345][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.347][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 06:56:40.349][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.350][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 06:56:40.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:40.355][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.357][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.359][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.360][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:56:40.362][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:40.363][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.364][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 06:56:40.366][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:40.367][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.368][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.370][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.371][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:40.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:40.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.379][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.381][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:40.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:40.385][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.386][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.388][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 06:56:40.390][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.391][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:56:40.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:40.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.398][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.400][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.401][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:56:40.403][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:40.404][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.406][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 06:56:40.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:40.408][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.410][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.411][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.413][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:40.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.417][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:40.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.422][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:40.425][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:40.426][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.427][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:40.429][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:40.430][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.496][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.DEBUG[2025-08-29 06:56:40.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.548][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 06:56:40.550][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 06:56:40.552][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 06:56:40.554][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 06:56:40.556][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:56:40.558][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 06:56:40.560][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 06:56:40.562][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 06:56:40.564][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 06:56:40.566][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 06:56:40.568][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:56:40.570][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 06:56:40.572][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 06:56:40.574][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 06:56:40.576][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 06:56:40.578][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 06:56:40.580][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 06:56:40.582][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 06:56:40.584][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:56:40.586][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 06:56:40.588][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 06:56:40.589][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 06:56:40.591][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 06:56:40.593][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 06:56:40.595][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 06:56:40.597][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 06:56:40.599][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 06:56:40.601][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 06:56:40.603][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 06:56:40.605][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 06:56:40.607][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 06:56:40.609][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 06:56:40.611][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 06:56:40.613][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 06:56:40.615][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 06:56:40.617][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 06:56:40.619][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 06:56:40.621][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 06:56:40.623][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 06:56:40.625][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 06:56:40.627][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 06:56:40.629][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 06:56:40.631][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 06:56:40.633][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 06:56:40.635][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 06:56:40.637][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 06:56:40.639][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 06:56:40.641][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 06:56:40.643][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 06:56:40.645][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 06:56:40.647][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 06:56:40.649][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 06:56:40.651][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 06:56:40.653][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 06:56:40.655][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 06:56:40.657][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 06:56:40.659][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 06:56:40.661][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 06:56:40.663][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 06:56:40.665][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 06:56:40.667][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 06:56:40.669][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 06:56:40.671][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 06:56:40.673][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 06:56:40.675][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 06:56:40.677][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 06:56:40.679][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:56:40.681][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:56:40.683][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 06:56:40.685][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 06:56:40.687][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 06:56:40.689][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 06:56:40.691][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 06:56:40.693][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 06:56:40.695][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 06:56:40.697][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 06:56:40.707][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 06:56:40.710][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 06:56:40.712][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 06:56:40.714][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 06:56:40.716][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 06:56:40.718][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 06:56:40.720][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 06:56:40.722][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 06:56:40.724][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:56:40.726][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:40.727][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.730][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.762][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[2025-08-29 06:56:40.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.806][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[2025-08-29 06:56:40.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.832][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[2025-08-29 06:56:40.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.841][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[2025-08-29 06:56:40.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:40.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:40.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:40.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:40.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:40.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:40.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:40.888][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 06:56:40.890][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 06:56:40.892][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.894][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.895][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:40.898][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.899][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.901][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.902][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 06:56:40.904][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 06:56:40.905][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:40.907][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.909][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 06:56:40.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 06:56:40.912][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 06:56:40.913][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:40.915][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:40.915][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:40.915][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:40.916][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 06:56:40.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.920][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:40.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:40.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:40.925][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:40.926][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:56:40.926][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 06:56:40.928][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:40.929][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:40.931][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:40.932][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 06:56:40.932][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 06:56:40.950][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:56:40.953][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:56:40.956][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 06:56:40.958][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:56:40.960][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:56:40.963][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:56:40.968][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 06:56:40.969][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 06:56:40.971][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 06:56:40.973][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 06:56:40.975][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:56:40.976][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:56:40.978][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 06:56:40.980][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 06:56:40.982][biodb::testThat]
biodb.INFO [2025-08-29 06:56:40.983][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-08-29 06:56:40.984][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:40.986][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:40.991][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 06:56:40.996][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:40.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 06:56:41.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.002][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 06:56:41.006][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.011][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.013][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 06:56:41.014][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.017][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 06:56:41.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.034][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.038][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.040][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 06:56:41.042][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.045][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 06:56:41.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.096][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[2025-08-29 06:56:41.103][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.107][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.109][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 06:56:41.111][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.113][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 06:56:41.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.128][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[2025-08-29 06:56:41.130][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 06:56:41.138][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.140][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 06:56:41.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.175][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.179][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 06:56:41.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.184][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 06:56:41.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.211][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.216][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 06:56:41.220][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.222][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 06:56:41.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.240][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.244][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.247][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-08-29 06:56:41.248][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.251][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-08-29 06:56:41.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 06:56:41.275][biodb::testThat]
biodb.INFO [2025-08-29 06:56:41.276][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-08-29 06:56:41.278][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:41.279][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:41.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.288][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.290][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2025-08-29 06:56:41.292][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.294][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2025-08-29 06:56:41.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.315][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:41.320][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:41.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2025-08-29 06:56:41.323][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:41.326][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2025-08-29 06:56:41.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:41.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 06:56:41.348][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 06:56:41.350][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 06:56:41.352][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 06:56:41.353][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 06:56:41.354][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:41.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:41.357][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.359][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 06:56:41.365][biodb::testContext]
biodb.INFO [2025-08-29 06:56:41.366][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:56:41.368][biodb::testContext] Test context - Test web services
biodb.INFO [2025-08-29 06:56:41.369][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:56:41.370][biodb::testContext]
biodb.INFO [2025-08-29 06:56:41.373][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:56:41.376][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 06:56:41.380][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:41.382][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 06:56:41.383][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 06:56:41.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.389][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 06:56:41.390][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 06:56:41.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.395][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 06:56:41.397][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 06:56:41.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.402][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 06:56:41.403][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 06:56:41.405][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 06:56:41.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.410][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 06:56:41.411][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 06:56:41.413][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 06:56:41.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.418][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 06:56:41.420][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 06:56:41.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.425][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 06:56:41.426][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 06:56:41.428][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 06:56:41.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.433][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 06:56:41.434][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 06:56:41.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.439][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 06:56:41.441][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 06:56:41.442][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 06:56:41.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.447][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:56:41.449][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 06:56:41.450][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 06:56:41.452][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 06:56:41.453][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 06:56:41.455][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 06:56:41.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.467][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[2025-08-29 06:56:41.469][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 06:56:41.470][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 06:56:41.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.476][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 06:56:41.477][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 06:56:41.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.482][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 06:56:41.484][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 06:56:41.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.489][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 06:56:41.490][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 06:56:41.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.496][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 06:56:41.497][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 06:56:41.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.502][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:56:41.504][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 06:56:41.509][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 06:56:41.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.514][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 06:56:41.516][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 06:56:41.517][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 06:56:41.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.522][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 06:56:41.564][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.565][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 06:56:41.567][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.569][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:41.570][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.572][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.573][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.575][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.576][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:56:41.578][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:41.579][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.581][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 06:56:41.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:41.584][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.586][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.587][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:41.587][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:41.587][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:41.587][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:56:41.587][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:56:41.589][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:41.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:41.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.598][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.600][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.601][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:41.603][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:41.604][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.606][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.608][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 06:56:41.610][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.612][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:56:41.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:41.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.618][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.619][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.621][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.622][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:56:41.624][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:41.625][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.627][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 06:56:41.628][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:41.630][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.631][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.633][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:41.633][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:41.633][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:41.633][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:56:41.633][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:56:41.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:41.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.638][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:41.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.642][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.644][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.645][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:41.647][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:41.648][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.650][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.651][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 06:56:41.654][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.655][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 06:56:41.657][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.658][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:41.660][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.661][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.663][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.664][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.666][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:56:41.667][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:41.669][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.670][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 06:56:41.672][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:41.673][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.676][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.678][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:41.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:41.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.686][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.687][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.689][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:41.690][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:41.692][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.693][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.695][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 06:56:41.697][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.699][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:56:41.700][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.702][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:41.712][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.715][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.717][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.719][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:56:41.720][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:41.722][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.723][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 06:56:41.725][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:41.726][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.728][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:41.729][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.730][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:41.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.735][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:41.736][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:41.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:41.739][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:41.740][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.742][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:41.743][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:41.745][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:41.746][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:41.748][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:41.750][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.780][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[2025-08-29 06:56:41.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.787][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[2025-08-29 06:56:41.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.827][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[2025-08-29 06:56:41.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:41.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:41.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:41.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:41.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:41.865][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[2025-08-29 06:56:41.866][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 06:56:41.868][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 06:56:41.870][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 06:56:41.872][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 06:56:41.875][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:56:41.877][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 06:56:41.879][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 06:56:41.881][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 06:56:41.883][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 06:56:41.885][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 06:56:41.887][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:56:41.889][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 06:56:41.891][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 06:56:41.893][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 06:56:41.896][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 06:56:41.898][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 06:56:41.900][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 06:56:41.902][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 06:56:41.904][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:56:41.906][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 06:56:41.908][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 06:56:41.910][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 06:56:41.912][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 06:56:41.914][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 06:56:41.916][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 06:56:41.918][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 06:56:41.920][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 06:56:41.922][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 06:56:41.924][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 06:56:41.926][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 06:56:41.928][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 06:56:41.930][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 06:56:41.932][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 06:56:41.934][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 06:56:41.936][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 06:56:41.938][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 06:56:41.940][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 06:56:41.942][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 06:56:41.944][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 06:56:41.946][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 06:56:41.948][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 06:56:41.950][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 06:56:42.203][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 06:56:42.206][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 06:56:42.208][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 06:56:42.210][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 06:56:42.212][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 06:56:42.214][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 06:56:42.216][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 06:56:42.218][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 06:56:42.220][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 06:56:42.222][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 06:56:42.224][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 06:56:42.226][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 06:56:42.228][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 06:56:42.230][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 06:56:42.232][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 06:56:42.234][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 06:56:42.236][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 06:56:42.238][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 06:56:42.240][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 06:56:42.242][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 06:56:42.244][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 06:56:42.246][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 06:56:42.247][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 06:56:42.249][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 06:56:42.251][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:56:42.253][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:56:42.255][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 06:56:42.257][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 06:56:42.259][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 06:56:42.261][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 06:56:42.263][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 06:56:42.265][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 06:56:42.267][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 06:56:42.269][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 06:56:42.271][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 06:56:42.273][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 06:56:42.275][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 06:56:42.277][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 06:56:42.279][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 06:56:42.281][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 06:56:42.283][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 06:56:42.285][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 06:56:42.287][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:56:42.288][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:42.290][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.292][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.293][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[2025-08-29 06:56:42.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.336][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[2025-08-29 06:56:42.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.440][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 06:56:42.442][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 06:56:42.452][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.453][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.456][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:42.457][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.460][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.461][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 06:56:42.463][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 06:56:42.464][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:42.465][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.467][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 06:56:42.468][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 06:56:42.470][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 06:56:42.471][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.472][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:42.472][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:42.472][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:42.474][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 06:56:42.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.478][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:42.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.482][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.483][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:56:42.483][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 06:56:42.485][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:42.486][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:42.487][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.489][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 06:56:42.489][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 06:56:42.497][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:56:42.499][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:56:42.502][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 06:56:42.504][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:56:42.506][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:56:42.508][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:56:42.513][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 06:56:42.514][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 06:56:42.516][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 06:56:42.518][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 06:56:42.520][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:56:42.521][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:56:42.523][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 06:56:42.524][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 06:56:42.526][biodb::testThat]
biodb.INFO [2025-08-29 06:56:42.527][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-08-29 06:56:42.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:42.530][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:42.534][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 06:56:42.539][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:42.541][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 06:56:42.543][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:42.545][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 06:56:42.549][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:42.553][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:42.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-08-29 06:56:42.557][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:42.559][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2025-08-29 06:56:42.569][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 06:56:42.571][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 06:56:42.573][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 06:56:42.574][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 06:56:42.575][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:42.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:42.577][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.580][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 06:56:42.586][biodb::testContext]
biodb.INFO [2025-08-29 06:56:42.587][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:56:42.588][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-08-29 06:56:42.590][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 06:56:42.591][biodb::testContext]
biodb.INFO [2025-08-29 06:56:42.594][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:56:42.596][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 06:56:42.601][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:42.602][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 06:56:42.604][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 06:56:42.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.609][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 06:56:42.610][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 06:56:42.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.615][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 06:56:42.617][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 06:56:42.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.622][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 06:56:42.623][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 06:56:42.625][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 06:56:42.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.630][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 06:56:42.631][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 06:56:42.633][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 06:56:42.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.638][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 06:56:42.639][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 06:56:42.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.644][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 06:56:42.646][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 06:56:42.647][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 06:56:42.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.652][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 06:56:42.653][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 06:56:42.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.658][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 06:56:42.660][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 06:56:42.661][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 06:56:42.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.666][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:56:42.668][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 06:56:42.669][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 06:56:42.671][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 06:56:42.672][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 06:56:42.673][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 06:56:42.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.678][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 06:56:42.680][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 06:56:42.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.685][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 06:56:42.686][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 06:56:42.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.692][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 06:56:42.693][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 06:56:42.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.705][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 06:56:42.707][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 06:56:42.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.711][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[2025-08-29 06:56:42.713][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 06:56:42.714][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 06:56:42.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.719][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 06:56:42.720][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 06:56:42.725][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 06:56:42.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.730][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 06:56:42.732][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 06:56:42.733][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 06:56:42.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.738][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 06:56:42.779][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.781][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 06:56:42.782][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.783][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:42.785][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.786][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.787][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.789][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.790][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:56:42.791][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:42.793][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.794][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 06:56:42.795][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:42.797][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.798][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.799][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:42.799][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:42.799][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:42.799][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:56:42.799][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:56:42.801][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:42.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:42.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.808][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.810][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:42.812][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:42.813][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.815][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.816][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 06:56:42.819][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.820][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:56:42.822][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.823][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:42.824][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.826][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.827][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.828][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.830][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:56:42.831][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:42.833][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.834][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 06:56:42.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:42.837][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.838][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.839][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:42.839][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:42.839][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:42.839][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 06:56:42.839][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 06:56:42.841][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:42.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:42.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.850][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:42.853][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:42.854][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.855][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.857][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 06:56:42.860][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.861][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 06:56:42.862][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:42.865][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.868][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.871][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 06:56:42.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:42.874][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.875][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 06:56:42.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:42.878][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.879][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.880][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.882][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:42.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.886][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:42.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.890][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.891][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:42.894][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:42.895][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.896][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.898][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 06:56:42.901][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.902][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 06:56:42.903][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.905][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:42.906][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.907][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.909][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.910][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.912][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 06:56:42.913][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:42.914][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.916][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 06:56:42.917][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:42.919][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.920][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:42.921][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.923][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 06:56:42.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.925][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:42.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:42.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:42.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:42.932][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.933][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:42.935][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:42.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:42.937][self$setPropertyValue]
biodb.DEBUG[2025-08-29 06:56:42.946][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:42.947][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:42.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:42.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:42.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:42.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:42.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.011][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[2025-08-29 06:56:43.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.024][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[2025-08-29 06:56:43.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.056][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 06:56:43.058][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 06:56:43.060][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 06:56:43.062][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 06:56:43.064][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:56:43.066][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 06:56:43.068][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 06:56:43.070][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 06:56:43.072][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 06:56:43.074][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 06:56:43.076][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:56:43.079][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 06:56:43.080][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 06:56:43.082][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 06:56:43.084][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 06:56:43.086][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 06:56:43.088][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 06:56:43.090][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 06:56:43.092][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:56:43.094][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 06:56:43.096][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 06:56:43.098][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 06:56:43.100][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 06:56:43.102][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 06:56:43.104][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 06:56:43.106][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 06:56:43.108][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 06:56:43.110][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 06:56:43.111][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 06:56:43.113][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 06:56:43.115][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 06:56:43.117][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 06:56:43.119][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 06:56:43.121][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 06:56:43.123][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 06:56:43.125][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 06:56:43.127][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 06:56:43.129][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 06:56:43.131][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 06:56:43.133][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 06:56:43.135][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 06:56:43.137][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 06:56:43.139][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 06:56:43.141][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 06:56:43.143][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 06:56:43.145][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 06:56:43.147][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 06:56:43.149][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 06:56:43.151][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 06:56:43.153][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 06:56:43.155][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 06:56:43.157][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 06:56:43.159][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 06:56:43.160][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 06:56:43.162][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 06:56:43.164][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 06:56:43.166][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 06:56:43.168][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 06:56:43.170][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 06:56:43.172][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 06:56:43.174][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 06:56:43.176][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 06:56:43.178][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 06:56:43.180][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 06:56:43.182][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 06:56:43.191][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 06:56:43.193][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:56:43.195][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:56:43.197][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 06:56:43.199][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 06:56:43.200][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 06:56:43.202][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 06:56:43.204][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 06:56:43.206][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 06:56:43.208][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 06:56:43.210][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 06:56:43.212][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 06:56:43.214][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 06:56:43.216][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 06:56:43.218][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 06:56:43.220][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 06:56:43.222][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 06:56:43.223][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 06:56:43.226][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 06:56:43.227][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 06:56:43.229][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 06:56:43.230][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.232][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.251][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.DEBUG[2025-08-29 06:56:43.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.293][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[2025-08-29 06:56:43.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 06:56:43.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 06:56:43.380][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 06:56:43.382][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 06:56:43.385][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:43.386][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 06:56:43.387][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:43.389][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 06:56:43.390][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:43.391][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 06:56:43.393][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:43.394][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 06:56:43.395][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 06:56:43.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 06:56:43.398][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:43.400][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 06:56:43.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 06:56:43.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 06:56:43.404][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 06:56:43.405][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 06:56:43.405][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 06:56:43.405][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 06:56:43.407][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 06:56:43.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:43.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:43.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 06:56:43.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 06:56:43.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 06:56:43.414][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 06:56:43.416][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 06:56:43.416][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 06:56:43.417][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 06:56:43.418][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 06:56:43.420][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 06:56:43.427][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 06:56:43.427][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 06:56:43.436][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 06:56:43.439][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 06:56:43.441][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 06:56:43.443][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 06:56:43.445][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 06:56:43.447][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 06:56:43.452][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 06:56:43.453][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 06:56:43.455][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 06:56:43.457][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 06:56:43.459][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:56:43.460][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 06:56:43.462][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 06:56:43.463][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 06:56:43.465][biodb::testThat]
biodb.INFO [2025-08-29 06:56:43.466][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-08-29 06:56:43.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 06:56:43.469][biodb::testThat]
biodb.DEBUG[2025-08-29 06:56:43.473][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 06:56:43.477][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:43.479][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 06:56:43.481][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:43.483][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 06:56:43.487][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 06:56:43.491][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 06:56:43.493][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-08-29 06:56:43.495][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:43.497][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-08-29 06:56:43.502][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-08-29 06:56:43.504][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 06:56:43.506][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-08-29 06:56:43.508][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 06:56:43.512][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2025-08-29 06:56:43.513][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 06:56:43.515][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 06:56:43.516][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 06:56:43.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 06:56:43.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 06:56:43.537][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.538][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.541][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.549][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:43.551][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:43.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.553][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.556][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 06:56:43.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 06:56:43.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.562][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:43.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:43.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.566][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 06:56:43.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 06:56:43.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.574][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 06:56:43.575][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 06:56:43.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.578][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.580][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 06:56:43.582][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 06:56:43.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.585][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:43.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:43.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.591][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.593][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:43.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 06:56:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.599][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:43.601][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:43.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.603][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.606][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 06:56:43.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 06:56:43.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.612][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:43.613][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:43.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.616][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:43.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 06:56:43.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.624][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:43.625][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:43.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.628][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 06:56:43.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 06:56:43.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.637][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:43.639][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:43.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.641][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 06:56:43.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 06:56:43.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.650][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:43.651][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:43.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.654][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.656][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 06:56:43.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 06:56:43.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:43.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:43.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:43.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:43.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 06:56:43.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 06:56:43.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 06:56:43.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 06:56:43.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 06:56:43.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 06:56:43.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 06:56:43.728][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-08-29 06:56:43.733][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 06:56:43.735][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 06:56:43.736][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 06:56:43.737][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 06:56:43.739][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 06:56:43.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 06:56:43.741][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 06:56:43.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 06:56:43.744][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 06:56:43.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 362 ]
>
> proc.time()
user system elapsed
22.195 0.902 47.806
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.179 | 0.121 | 6.517 | |
| ChebiEntry | 0.223 | 0.000 | 0.223 | |