Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-06 12:03 -0400 (Mon, 06 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 208/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbChebi 1.15.1 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: biodbChebi |
Version: 1.15.1 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings biodbChebi_1.15.1.tar.gz |
StartedAt: 2025-10-05 21:38:00 -0400 (Sun, 05 Oct 2025) |
EndedAt: 2025-10-05 21:39:36 -0400 (Sun, 05 Oct 2025) |
EllapsedTime: 95.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbChebi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings biodbChebi_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/biodbChebi.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘biodbChebi/DESCRIPTION’ ... OK * this is package ‘biodbChebi’ version ‘1.15.1’ * 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 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** this is package ‘biodbChebi’ version ‘1.15.1’ ** 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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbChebi) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbChebi") biodb.INFO [2025-10-05 21:39:00.494][biodb::testContext] biodb.INFO [2025-10-05 21:39:00.497][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:00.498][biodb::testContext] Test context - Generic tests biodb.INFO [2025-10-05 21:39:00.499][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:00.500][biodb::testContext] biodb.INFO [2025-10-05 21:39:00.508][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:00.510][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2025-10-05 21:39:00.519][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:00.520][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-10-05 21:39:00.521][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-10-05 21:39:00.522][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.526][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-10-05 21:39:00.548][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-10-05 21:39:00.550][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.552][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[2025-10-05 21:39:00.553][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-10-05 21:39:00.554][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-10-05 21:39:00.555][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.570][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-10-05 21:39:00.571][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-10-05 21:39:00.572][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-10-05 21:39:00.573][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.576][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-10-05 21:39:00.578][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-10-05 21:39:00.579][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-10-05 21:39:00.580][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.583][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-10-05 21:39:00.584][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-10-05 21:39:00.585][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.589][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-10-05 21:39:00.590][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-10-05 21:39:00.592][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-10-05 21:39:00.593][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.597][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-10-05 21:39:00.599][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-10-05 21:39:00.600][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.603][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-10-05 21:39:00.604][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-10-05 21:39:00.605][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-10-05 21:39:00.606][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.609][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:00.610][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-10-05 21:39:00.612][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-10-05 21:39:00.613][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-10-05 21:39:00.614][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-10-05 21:39:00.615][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-10-05 21:39:00.616][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.619][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-10-05 21:39:00.620][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-10-05 21:39:00.621][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.624][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-10-05 21:39:00.626][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-10-05 21:39:00.627][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.630][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-10-05 21:39:00.631][self$set] Set key offline to FALSE. biodb.DEBUG[2025-10-05 21:39:00.632][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.635][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-10-05 21:39:00.636][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-10-05 21:39:00.637][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-10-05 21:39:00.638][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.641][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:00.642][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-10-05 21:39:00.654][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-10-05 21:39:00.655][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.663][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-10-05 21:39:00.669][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-10-05 21:39:00.671][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-10-05 21:39:00.672][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.680][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-10-05 21:39:00.732][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.759][self$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[2025-10-05 21:39:00.761][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.762][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:00.764][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.765][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:00.767][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:00.770][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:00.772][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:00.773][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.775][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-10-05 21:39:00.776][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:00.778][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.780][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.781][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:00.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:00.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:00.781][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:00.781][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:00.783][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:00.784][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.787][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:00.788][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.791][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:00.793][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.794][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:00.795][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:00.797][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.798][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.800][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-10-05 21:39:00.803][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.804][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:00.806][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.807][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:00.809][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.810][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:00.812][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.813][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:00.814][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:00.816][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:00.817][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.819][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-10-05 21:39:00.820][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:00.822][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.823][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.825][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:00.825][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:00.825][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:00.825][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:00.825][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:00.826][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:00.828][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.831][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:00.832][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.835][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:00.836][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.838][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:00.839][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:00.840][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.842][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.844][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-10-05 21:39:00.846][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.848][self$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[2025-10-05 21:39:00.849][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.851][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:00.852][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.854][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:00.855][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.857][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:00.858][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:00.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:00.861][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.863][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-10-05 21:39:00.864][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:00.866][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.867][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.869][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.870][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:00.872][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.874][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:00.878][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.884][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:00.885][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.887][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:00.895][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:00.897][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.898][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.900][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-10-05 21:39:00.903][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.911][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:00.912][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.914][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:00.915][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.917][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:00.918][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:00.921][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:00.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:00.924][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.926][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-10-05 21:39:00.927][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:00.928][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.930][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:00.931][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.933][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:00.934][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.937][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:00.938][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:00.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:00.941][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:00.943][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.944][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:00.945][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:00.947][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:00.948][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:00.954][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:00.955][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.958][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:00.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:00.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.965][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:00.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:00.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.971][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:00.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:00.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.978][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:00.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:00.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.985][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:00.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:00.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.992][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:00.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:00.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:00.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:00.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:00.998][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.005][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.012][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.018][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.024][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[2025-10-05 21:39:01.025][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.034][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.040][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.051][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[2025-10-05 21:39:01.052][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.057][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[2025-10-05 21:39:01.058][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.065][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.075][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-10-05 21:39:01.081][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-10-05 21:39:01.083][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-10-05 21:39:01.085][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-10-05 21:39:01.086][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:01.088][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-10-05 21:39:01.090][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-10-05 21:39:01.092][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-10-05 21:39:01.093][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-10-05 21:39:01.095][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-10-05 21:39:01.097][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:01.098][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-10-05 21:39:01.100][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-10-05 21:39:01.102][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-10-05 21:39:01.104][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-10-05 21:39:01.105][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-10-05 21:39:01.107][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-10-05 21:39:01.109][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-10-05 21:39:01.110][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:01.112][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-10-05 21:39:01.114][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-10-05 21:39:01.116][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-10-05 21:39:01.117][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-10-05 21:39:01.119][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-10-05 21:39:01.121][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-10-05 21:39:01.122][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-10-05 21:39:01.124][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-10-05 21:39:01.126][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-10-05 21:39:01.128][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-10-05 21:39:01.129][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-10-05 21:39:01.131][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-10-05 21:39:01.133][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-10-05 21:39:01.134][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-10-05 21:39:01.136][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-10-05 21:39:01.138][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-10-05 21:39:01.139][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-10-05 21:39:01.141][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-10-05 21:39:01.143][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-10-05 21:39:01.145][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-10-05 21:39:01.146][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-10-05 21:39:01.148][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-10-05 21:39:01.150][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-10-05 21:39:01.151][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-10-05 21:39:01.153][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-10-05 21:39:01.155][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-10-05 21:39:01.157][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-10-05 21:39:01.158][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-10-05 21:39:01.160][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-10-05 21:39:01.162][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-10-05 21:39:01.163][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-10-05 21:39:01.165][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-10-05 21:39:01.167][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-10-05 21:39:01.168][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-10-05 21:39:01.170][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-10-05 21:39:01.172][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-10-05 21:39:01.173][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-10-05 21:39:01.175][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-10-05 21:39:01.177][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-10-05 21:39:01.179][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-10-05 21:39:01.180][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-10-05 21:39:01.182][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-10-05 21:39:01.184][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-10-05 21:39:01.185][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-10-05 21:39:01.187][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-10-05 21:39:01.189][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-10-05 21:39:01.190][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-10-05 21:39:01.192][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:01.194][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:01.196][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-10-05 21:39:01.197][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-10-05 21:39:01.199][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-10-05 21:39:01.201][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-10-05 21:39:01.202][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-10-05 21:39:01.204][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-10-05 21:39:01.206][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-10-05 21:39:01.207][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-10-05 21:39:01.209][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-10-05 21:39:01.211][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-10-05 21:39:01.213][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-10-05 21:39:01.223][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-10-05 21:39:01.225][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-10-05 21:39:01.226][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-10-05 21:39:01.228][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-10-05 21:39:01.236][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-10-05 21:39:01.237][initialize] This is biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:01.242][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:01.243][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.245][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.246][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[2025-10-05 21:39:01.252][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.259][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.266][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.DEBUG[2025-10-05 21:39:01.267][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.275][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.283][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.290][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.297][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.DEBUG[2025-10-05 21:39:01.298][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.306][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.313][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.320][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[2025-10-05 21:39:01.321][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.328][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[2025-10-05 21:39:01.329][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.336][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[2025-10-05 21:39:01.337][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.344][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.353][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.360][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.368][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:01.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:01.376][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml". biodb.DEBUG[2025-10-05 21:39:01.389][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-10-05 21:39:01.392][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:01.393][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-10-05 21:39:01.394][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:01.395][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:01.397][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:01.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:01.399][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:01.400][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-10-05 21:39:01.402][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-10-05 21:39:01.403][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:01.404][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:01.405][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-10-05 21:39:01.406][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-10-05 21:39:01.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-10-05 21:39:01.409][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-10-05 21:39:01.410][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:01.410][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:01.410][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:01.411][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-10-05 21:39:01.413][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:01.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:01.415][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:01.416][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:01.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:01.418][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:01.420][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-10-05 21:39:01.420][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-10-05 21:39:01.421][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:01.422][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:01.424][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:01.425][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-10-05 21:39:01.425][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-10-05 21:39:01.434][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:01.436][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:01.438][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-10-05 21:39:01.440][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:01.442][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:01.444][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:01.474][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-10-05 21:39:01.494][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-10-05 21:39:01.506][biodb::testThat] biodb.INFO [2025-10-05 21:39:01.524][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2025-10-05 21:39:01.525][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:01.526][biodb::testThat] biodb.TRACE[2025-10-05 21:39:01.534][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml". biodb.DEBUG[2025-10-05 21:39:01.537][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:01.548][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:01.573][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:01.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:01.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:01.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:01.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:01.599][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:01.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:01.616][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.618][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.620][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.622][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.662][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:01.664][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:01.665][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.667][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.714][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:01.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:01.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.722][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:01.724][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:01.725][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.727][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:01.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:01.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.735][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:01.737][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:01.739][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.740][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:01.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:01.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.749][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:01.750][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:01.752][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.753][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:01.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:01.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.762][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:01.763][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:01.765][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.766][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.768][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:01.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:01.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.775][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:01.776][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:01.778][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.779][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.781][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:01.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:01.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.788][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:01.789][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:01.791][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.792][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:01.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:01.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.801][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:01.802][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:01.804][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.805][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:01.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:01.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.814][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:01.816][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:01.817][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.819][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.821][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:01.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:01.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.827][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:01.829][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:01.830][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.832][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:01.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:01.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:01.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:01.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:01.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:01.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:01.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:01.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:01.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:01.978][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440. biodb.TRACE[2025-10-05 21:39:01.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:01.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:01.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:01.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:01.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:01.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:01.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.063][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-10-05 21:39:02.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-10-05 21:39:02.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-10-05 21:39:02.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-10-05 21:39:02.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.076][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-10-05 21:39:02.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-10-05 21:39:02.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.082][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-10-05 21:39:02.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-10-05 21:39:02.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.231][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.232][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.234][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.235][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.276][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.277][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.279][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.280][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:02.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:02.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:02.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:02.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:02.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:02.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.322][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:02.323][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:02.325][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.326][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:02.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:02.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:02.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:02.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:02.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:02.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.361][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:02.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:02.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.368][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:02.369][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:02.371][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.372][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.374][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:02.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:02.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.411][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.413][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.414][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.416][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.455][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.457][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.459][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.460][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.548][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:02.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:02.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.555][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:02.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:02.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.561][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:02.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:02.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.567][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:02.569][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:02.570][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.572][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.573][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:02.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:02.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.591][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-10-05 21:39:02.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:02.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.598][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-10-05 21:39:02.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:02.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-10-05 21:39:02.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:02.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.611][ef$get] Asked field names are: n.stars. biodb.TRACE[2025-10-05 21:39:02.612][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:02.614][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.615][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.617][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-10-05 21:39:02.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:02.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.635][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.641][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.654][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.655][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.657][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.659][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.660][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.678][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:02.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:02.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:02.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:02.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.691][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:02.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:02.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.697][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:02.699][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:02.700][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.702][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:02.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:02.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.740][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.742][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.744][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.745][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:02.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:02.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:02.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:02.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:02.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:02.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.783][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:02.785][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:02.787][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.788][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:02.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:02.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.807][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:02.810][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:02.811][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.812][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.820][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:02.822][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:02.824][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.825][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.841][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:02.843][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:02.844][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.846][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.853][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:02.855][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:02.857][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.858][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.866][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:02.868][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:02.869][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.871][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.878][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.880][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:02.882][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.883][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.890][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.892][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:02.894][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.895][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.902][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.904][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:02.905][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.907][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.914][ef$get] Asked field names are: n.stars. biodb.TRACE[2025-10-05 21:39:02.916][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:02.917][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.919][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.926][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:02.928][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:02.930][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.931][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:02.938][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:02.940][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:02.942][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:02.944][ef$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:02.956][biodb::testThat] biodb.INFO [2025-10-05 21:39:02.957][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2025-10-05 21:39:02.959][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:02.961][biodb::testThat] biodb.DEBUG[2025-10-05 21:39:02.986][private$loadEntries] Creating entries from ids [1]: "15440". biodb.DEBUG[2025-10-05 21:39:02.990][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:02.995][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:03.006][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml. biodb.DEBUG[2025-10-05 21:39:03.008][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:03.052][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:03.054][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:03.057][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:03.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:03.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:03.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:03.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:03.070][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:03.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:03.075][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.077][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.079][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.080][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.118][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:03.119][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:03.121][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.122][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:03.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:03.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.129][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:03.131][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:03.139][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.141][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:03.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:03.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.148][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:03.150][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:03.151][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.152][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:03.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:03.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.160][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:03.161][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:03.162][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.164][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:03.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:03.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.171][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:03.172][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:03.174][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.175][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.177][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:03.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:03.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.183][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:03.184][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.185][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.187][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.188][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:03.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.194][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:03.196][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:03.197][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.198][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:03.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:03.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.206][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.207][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.208][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.210][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.212][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.218][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:03.219][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:03.220][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.222][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.223][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:03.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:03.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.229][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:03.231][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:03.232][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.233][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.235][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:03.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:03.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:03.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:03.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:03.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:03.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:03.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:03.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:03.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:03.295][self$createEntryFromContent] Accession numbers: 15440. biodb.TRACE[2025-10-05 21:39:03.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2025-10-05 21:39:03.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2025-10-05 21:39:03.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2025-10-05 21:39:03.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2025-10-05 21:39:03.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2025-10-05 21:39:03.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2025-10-05 21:39:03.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:03.322][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.324][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2025-10-05 21:39:03.325][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:03.327][biodb::testThat] biodb.TRACE[2025-10-05 21:39:03.331][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.332][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.334][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.335][ef$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:03.336][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name". biodb.TRACE[2025-10-05 21:39:03.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:03.398][function(conn, opt)] With value "squalene". sched.DEBUG[2025-10-05 21:39:03.406][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". fscache.INFO [2025-10-05 21:39:03.432][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:03.440][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content. sched.DEBUG[2025-10-05 21:39:03.442][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:03.467][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". fscache.INFO [2025-10-05 21:39:03.552][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:03.563][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:03.568][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:03.573][function(conn, opt)] With found IDs [1]: "15440". biodb.TRACE[2025-10-05 21:39:03.596][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:03.598][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:03.599][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.600][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.601][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.603][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.604][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.605][ef$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:03.610][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.611][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2025-10-05 21:39:03.612][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:03.614][biodb::testThat] biodb.TRACE[2025-10-05 21:39:03.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:03.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:03.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:03.740][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". fscache.INFO [2025-10-05 21:39:03.744][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:03.748][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:03.749][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.INFO [2025-10-05 21:39:03.768][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.770][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2025-10-05 21:39:03.771][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:03.772][biodb::testThat] biodb.TRACE[2025-10-05 21:39:03.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:03.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:03.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:03.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:03.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:03.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:03.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.813][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:03.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:03.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.828][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.833][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-10-05 21:39:03.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-10-05 21:39:03.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.842][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-10-05 21:39:03.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-10-05 21:39:03.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:03.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:03.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:03.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:03.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:03.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:03.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:03.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:03.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.913][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-10-05 21:39:03.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.922][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-10-05 21:39:03.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-10-05 21:39:03.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:03.927][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-10-05 21:39:03.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-10-05 21:39:03.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:03.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:03.938][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.939][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2025-10-05 21:39:03.941][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:03.942][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.951][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.952][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2025-10-05 21:39:03.953][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:03.955][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.963][biodb::testThat] biodb.INFO [2025-10-05 21:39:03.965][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2025-10-05 21:39:03.966][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:03.967][biodb::testThat] biodb.DEBUG[2025-10-05 21:39:03.971][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440". sched.TRACE[2025-10-05 21:39:04.677][try_get_rcurl_content] Using RCurl package for sending request (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440). biodb.INFO [2025-10-05 21:39:05.967][biodb::testThat] biodb.INFO [2025-10-05 21:39:05.968][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2025-10-05 21:39:05.969][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:05.970][biodb::testThat] biodb.TRACE[2025-10-05 21:39:05.977][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:05.979][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:05.980][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:05.981][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:05.982][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:05.983][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:05.984][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:05.985][ef$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:05.988][biodb::testThat] biodb.INFO [2025-10-05 21:39:05.989][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2025-10-05 21:39:05.990][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:05.991][biodb::testThat] biodb.TRACE[2025-10-05 21:39:06.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:06.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:06.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:06.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:06.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:06.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:06.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:06.197][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". fscache.INFO [2025-10-05 21:39:06.201][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:06.206][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:06.208][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:06.312][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". fscache.INFO [2025-10-05 21:39:06.315][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:06.319][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:06.320][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.TRACE[2025-10-05 21:39:06.336][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-10-05 21:39:06.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-10-05 21:39:06.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:06.389][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". fscache.INFO [2025-10-05 21:39:06.396][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:06.403][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content. sched.DEBUG[2025-10-05 21:39:06.404][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:06.409][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:06.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:06.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:06.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:06.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:06.428][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:06.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:06.434][private$loadEntries] Creating entries from ids [1]: "192288". biodb.DEBUG[2025-10-05 21:39:06.522][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:06.524][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:06.531][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml. biodb.DEBUG[2025-10-05 21:39:06.536][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:06.537][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:06.538][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:06.540][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:06.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:06.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:06.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:06.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:06.549][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:06.550][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[2025-10-05 21:39:06.553][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.554][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.556][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.557][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.563][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:06.564][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:06.565][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.566][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.568][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:06.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.573][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:06.574][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:06.575][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.576][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:06.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:06.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.583][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:06.584][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:06.585][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.586][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:06.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:06.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.592][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:06.594][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:06.595][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.596][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:06.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:06.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.602][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:06.610][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:06.612][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.613][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.614][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:06.616][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.617][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.618][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.619][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:06.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.624][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.625][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.626][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.627][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.633][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:06.635][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:06.636][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.637][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:06.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:06.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.643][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:06.645][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:06.646][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.647][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.648][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:06.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:06.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.653][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:06.654][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:06.655][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.656][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.658][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:06.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:06.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:06.710][self$createEntryFromContent] Accession numbers: 192288. biodb.TRACE[2025-10-05 21:39:06.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:06.737][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:06.740][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:06.746][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content. sched.DEBUG[2025-10-05 21:39:06.748][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:06.769][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:06.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:06.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:06.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:06.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:06.779][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:06.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:06.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:06.796][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:06.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:06.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:06.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:06.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:06.815][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:06.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:06.817][private$loadEntries] Creating entries from ids [1]: "209892". biodb.DEBUG[2025-10-05 21:39:06.818][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:06.820][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:06.828][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml. biodb.DEBUG[2025-10-05 21:39:06.834][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:06.835][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:06.840][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:06.842][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:06.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:06.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:06.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:06.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:06.860][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:06.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:06.864][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.866][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.867][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.868][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.874][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:06.875][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:06.876][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.878][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.879][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:06.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:06.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.884][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:06.885][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:06.886][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.887][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.889][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:06.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:06.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.894][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:06.895][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:06.896][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.897][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:06.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:06.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.903][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:06.905][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:06.906][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.907][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:06.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:06.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.913][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:06.914][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:06.915][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.916][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.918][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:06.919][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.920][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.921][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.923][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:06.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:06.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.928][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.929][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.930][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.931][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:06.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.937][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:06.939][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:06.940][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.941][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:06.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:06.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.947][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:06.948][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:06.949][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.951][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.952][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:06.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:06.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.957][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:06.958][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:06.959][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.960][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:06.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:06.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:06.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:06.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:06.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:06.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:06.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.013][self$createEntryFromContent] Accession numbers: 209892. biodb.TRACE[2025-10-05 21:39:07.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:07.055][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". fscache.INFO [2025-10-05 21:39:07.058][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:07.063][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:07.064][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:07.067][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.078][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:07.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.097][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.110][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:07.113][private$loadEntries] Creating entries from ids [1]: "26747". biodb.DEBUG[2025-10-05 21:39:07.114][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:07.117][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:07.123][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml. biodb.DEBUG[2025-10-05 21:39:07.127][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:07.129][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:07.130][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:07.133][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.145][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:07.150][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.151][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.153][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.154][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.162][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:07.163][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:07.165][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.166][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.168][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:07.170][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:07.171][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.173][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.175][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:07.176][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:07.178][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.179][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.181][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:07.182][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:07.184][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.185][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.187][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.189][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.190][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.192][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.194][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:07.195][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.197][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.198][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.200][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.202][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.203][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.204][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.206][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.208][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.209][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.211][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.219][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.220][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.222][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.223][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.225][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.231][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:07.232][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:07.234][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.235][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.302][self$createEntryFromContent] Accession numbers: 26747. biodb.TRACE[2025-10-05 21:39:07.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.334][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.346][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:07.349][private$loadEntries] Creating entries from ids [1]: "59285". biodb.DEBUG[2025-10-05 21:39:07.350][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:07.352][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:07.360][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml. biodb.DEBUG[2025-10-05 21:39:07.362][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:07.364][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:07.366][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:07.368][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.381][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:07.387][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.388][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.390][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.391][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.400][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:07.401][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:07.403][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.404][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.406][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:07.408][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:07.409][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.411][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.413][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:07.414][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:07.416][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.417][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.419][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:07.424][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:07.425][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.426][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.427][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.428][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.430][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.431][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.432][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:07.433][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.435][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.436][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.437][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.438][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.439][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.441][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.442][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.443][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.445][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.446][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.452][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.454][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.455][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.456][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.457][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.462][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:07.463][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:07.465][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.466][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.522][self$createEntryFromContent] Accession numbers: 59285. biodb.TRACE[2025-10-05 21:39:07.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.546][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.556][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:07.558][private$loadEntries] Creating entries from ids [1]: "75174". biodb.DEBUG[2025-10-05 21:39:07.559][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:07.561][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:07.570][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml. biodb.DEBUG[2025-10-05 21:39:07.572][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:07.577][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:07.579][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:07.585][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.595][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:07.599][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.600][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.601][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.602][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.609][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:07.610][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:07.611][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.612][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.613][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:07.615][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:07.616][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.617][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.619][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:07.620][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:07.621][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.622][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.623][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:07.625][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:07.626][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.627][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.628][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.629][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.631][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.632][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.633][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:07.634][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.635][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.636][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.638][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.639][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.640][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.641][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.643][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.644][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.645][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.646][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.653][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.654][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.655][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.657][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.663][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:07.664][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:07.665][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.666][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.721][self$createEntryFromContent] Accession numbers: 75174. biodb.TRACE[2025-10-05 21:39:07.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:07.750][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.764][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:07.767][private$loadEntries] Creating entries from ids [1]: "15441". biodb.DEBUG[2025-10-05 21:39:07.768][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:07.769][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:07.780][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml. biodb.DEBUG[2025-10-05 21:39:07.782][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:07.787][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:07.793][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:07.795][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:07.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:07.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:07.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:07.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:07.818][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:07.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:07.826][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.831][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.832][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.833][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.844][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:07.849][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:07.850][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.851][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:07.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:07.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.865][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:07.867][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:07.868][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.869][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:07.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:07.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.888][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:07.889][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:07.890][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.895][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:07.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:07.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.905][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:07.906][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:07.907][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.912][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:07.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:07.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.923][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.924][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.925][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.926][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.928][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:07.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.932][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:07.934][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.935][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.936][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.937][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:07.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:07.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.942][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.943][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.944][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.945][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:07.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.952][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.953][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.954][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.955][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:07.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:07.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.962][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.963][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.964][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.965][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.966][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:07.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:07.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.971][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:07.972][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:07.973][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.974][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.976][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:07.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:07.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:07.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:07.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:07.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:07.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:07.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.033][self$createEntryFromContent] Accession numbers: 15441. biodb.TRACE[2025-10-05 21:39:08.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.048][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.062][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.063][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[2025-10-05 21:39:08.064][private$loadEntries] Creating entries from ids [1]: "15442". biodb.DEBUG[2025-10-05 21:39:08.066][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:08.067][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:08.080][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml. biodb.DEBUG[2025-10-05 21:39:08.082][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:08.087][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:08.089][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:08.091][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.102][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:08.106][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.108][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.109][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.110][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.116][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.118][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.119][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.120][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.126][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.127][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.128][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.129][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.131][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.135][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.137][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.138][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.139][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.145][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.146][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.147][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.148][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.154][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.155][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.157][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.158][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.159][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.164][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.165][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.166][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.167][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.168][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.173][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.174][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.175][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.177][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.183][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.184][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.185][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.186][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.192][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.193][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.195][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.196][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.197][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.202][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.203][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.204][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.205][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.207][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.270][self$createEntryFromContent] Accession numbers: 15442. biodb.TRACE[2025-10-05 21:39:08.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.290][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.303][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:08.306][private$loadEntries] Creating entries from ids [1]: "57310". biodb.DEBUG[2025-10-05 21:39:08.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:08.309][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:08.319][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml. biodb.DEBUG[2025-10-05 21:39:08.321][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:08.322][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:08.324][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:08.326][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.336][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:08.340][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.341][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.342][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.344][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.350][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.351][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.352][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.353][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.355][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.359][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.361][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.362][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.363][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.369][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.370][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.371][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.372][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.378][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.380][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.381][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.382][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.388][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.389][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.390][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.391][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.393][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.394][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.395][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.396][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.398][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.402][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.404][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.405][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.406][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.412][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.413][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.414][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.415][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.422][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.423][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.430][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.432][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.433][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.438][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.439][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.440][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.441][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.443][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.494][self$createEntryFromContent] Accession numbers: 57310. biodb.TRACE[2025-10-05 21:39:08.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.522][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:08.525][private$loadEntries] Creating entries from ids [1]: "66216". biodb.DEBUG[2025-10-05 21:39:08.526][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:08.528][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:08.541][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml. biodb.DEBUG[2025-10-05 21:39:08.543][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:08.546][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:08.548][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:08.550][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.560][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:08.563][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.565][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.566][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.567][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.573][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.574][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.575][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.577][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.578][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.583][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.584][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.585][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.586][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.593][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.594][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.595][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.596][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.603][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.604][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.605][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.606][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.612][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.613][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.615][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.616][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.617][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.618][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.619][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.621][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.622][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.627][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.628][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.629][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.630][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.643][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.644][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.645][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.646][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.653][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.654][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.655][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.656][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.662][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.664][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.665][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.666][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.667][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.718][self$createEntryFromContent] Accession numbers: 66216. biodb.TRACE[2025-10-05 21:39:08.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:08.733][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.744][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:08.746][private$loadEntries] Creating entries from ids [1]: "70860". biodb.DEBUG[2025-10-05 21:39:08.747][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:08.749][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:08.755][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml. biodb.DEBUG[2025-10-05 21:39:08.756][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:08.761][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:08.762][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:08.768][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:08.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:08.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:08.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:08.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:08.779][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:08.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:08.783][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.784][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.785][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.786][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.793][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.794][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.795][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.796][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.798][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:08.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:08.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.803][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.804][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.805][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.806][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:08.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:08.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.812][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.813][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.815][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.816][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:08.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:08.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.822][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.823][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.824][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.825][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:08.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:08.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.832][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.833][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:08.834][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.835][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.837][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.838][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.839][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.848][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.849][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:08.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:08.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.862][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.864][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.869][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.870][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:08.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.880][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.882][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.887][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.888][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:08.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:08.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.903][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.908][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.909][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.910][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.912][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:08.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:08.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.921][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.926][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.927][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.928][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.934][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:08.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:08.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:08.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:08.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:08.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:08.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:08.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.042][self$createEntryFromContent] Accession numbers: 70860. biodb.TRACE[2025-10-05 21:39:09.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.073][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.095][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.096][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[2025-10-05 21:39:09.098][private$loadEntries] Creating entries from ids [1]: "70861". biodb.DEBUG[2025-10-05 21:39:09.099][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:09.105][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:09.113][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml. biodb.DEBUG[2025-10-05 21:39:09.119][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:09.120][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:09.125][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:09.127][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.149][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:09.157][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.158][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.160][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.161][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.175][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.180][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.181][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.183][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.188][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.193][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.198][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.200][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.205][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.211][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:09.213][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:09.214][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.215][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:09.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:09.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.221][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:09.222][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:09.224][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.232][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:09.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:09.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.238][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:09.239][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:09.240][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.242][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.243][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:09.244][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.245][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.246][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.248][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:09.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.253][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.254][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.255][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.256][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.262][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:09.263][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:09.264][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.266][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:09.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:09.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.272][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:09.273][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:09.274][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.276][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.277][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:09.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:09.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.282][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:09.284][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:09.285][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.287][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.288][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:09.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:09.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.343][self$createEntryFromContent] Accession numbers: 70861. biodb.TRACE[2025-10-05 21:39:09.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.358][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.368][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:09.370][private$loadEntries] Creating entries from ids [1]: "78662". biodb.DEBUG[2025-10-05 21:39:09.371][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:09.373][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:09.387][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml. biodb.DEBUG[2025-10-05 21:39:09.388][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:09.392][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:09.394][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:09.401][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.414][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:09.418][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.420][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.421][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.423][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.430][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.432][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.434][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.435][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.437][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.443][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.444][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.446][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.447][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.449][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.462][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:09.463][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:09.464][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.466][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:09.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:09.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.474][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:09.475][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:09.476][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.478][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:09.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:09.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.485][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:09.487][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:09.488][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.490][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.492][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:09.493][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.494][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.496][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.498][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:09.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.503][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.505][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.506][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.508][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.515][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:09.517][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:09.518][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.520][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:09.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.528][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:09.529][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:09.531][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.532][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.534][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:09.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:09.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.540][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:09.542][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:09.543][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.545][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.547][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:09.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:09.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.613][self$createEntryFromContent] Accession numbers: 78662. biodb.TRACE[2025-10-05 21:39:09.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.633][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.645][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:09.648][private$loadEntries] Creating entries from ids [1]: "85084". biodb.DEBUG[2025-10-05 21:39:09.649][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:09.652][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:09.659][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml. biodb.DEBUG[2025-10-05 21:39:09.661][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:09.662][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:09.664][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:09.666][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.678][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:09.683][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.684][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.685][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.687][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.694][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.696][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.724][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.726][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.728][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.734][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.735][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.736][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.738][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.745][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:09.747][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:09.748][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.749][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.751][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:09.753][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:09.754][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.755][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.757][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:09.758][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:09.760][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.761][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.763][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:09.765][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.766][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.767][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.769][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:09.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.775][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.776][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.778][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.779][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:09.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.787][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:09.788][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:09.789][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.791][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:09.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:09.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.799][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:09.800][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:09.802][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.803][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.805][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:09.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:09.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.811][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:09.812][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:09.814][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.815][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:09.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.873][self$createEntryFromContent] Accession numbers: 85084. biodb.TRACE[2025-10-05 21:39:09.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:09.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:09.892][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.904][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:09.907][private$loadEntries] Creating entries from ids [1]: "85086". biodb.DEBUG[2025-10-05 21:39:09.908][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:09.910][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:09.917][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml. biodb.DEBUG[2025-10-05 21:39:09.919][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:09.921][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:09.922][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:09.925][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:09.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:09.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:09.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:09.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:09.938][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:09.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:09.942][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.944][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.946][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.947][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:09.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:09.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.955][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.957][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.958][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.966][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.968][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:09.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:09.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.975][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.977][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.978][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.979][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:09.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:09.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.987][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:09.989][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:09.991][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.992][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:09.994][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:09.995][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:09.997][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:09.998][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.000][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.002][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.003][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.005][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.007][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.008][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.010][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.011][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.013][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.019][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.021][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.022][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.024][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.032][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.033][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.035][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.036][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.045][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.046][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.048][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.049][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.051][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.058][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:10.059][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:10.061][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.062][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.126][self$createEntryFromContent] Accession numbers: 85086. biodb.TRACE[2025-10-05 21:39:10.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.144][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:10.159][private$loadEntries] Creating entries from ids [1]: "88123". biodb.DEBUG[2025-10-05 21:39:10.161][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:10.163][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:10.168][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml. biodb.DEBUG[2025-10-05 21:39:10.170][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:10.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:10.173][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:10.175][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.185][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:10.188][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.190][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.191][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.192][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.198][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.199][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.200][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.201][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.203][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.215][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.216][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.217][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.218][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.228][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.230][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.231][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.232][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.238][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.240][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.241][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.242][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.249][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.250][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.251][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.252][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.254][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.255][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.256][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.257][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.259][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.264][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.265][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.266][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.267][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.274][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.275][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.277][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.278][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.280][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.284][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.286][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.287][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.288][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.289][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.294][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:10.296][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:10.297][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.298][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:10.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:10.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.350][self$createEntryFromContent] Accession numbers: 88123. biodb.TRACE[2025-10-05 21:39:10.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.366][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.376][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:10.378][private$loadEntries] Creating entries from ids [1]: "134117". biodb.DEBUG[2025-10-05 21:39:10.379][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:10.381][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:10.390][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml. biodb.DEBUG[2025-10-05 21:39:10.391][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:10.393][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:10.394][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:10.396][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.406][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:10.409][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.411][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.418][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.419][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.426][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.428][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.429][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.430][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.436][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.437][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.438][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.439][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.441][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.446][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.447][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.448][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.449][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.455][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.456][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.457][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.458][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.472][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.474][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.475][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.476][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.478][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.480][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.481][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.482][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.484][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.490][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.491][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.493][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.494][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.501][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.502][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.503][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.505][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.512][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.513][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.514][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.515][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.517][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.522][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:10.524][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:10.525][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.526][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.528][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:10.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:10.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.584][self$createEntryFromContent] Accession numbers: 134117. biodb.TRACE[2025-10-05 21:39:10.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.601][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.613][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.614][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[2025-10-05 21:39:10.616][private$loadEntries] Creating entries from ids [1]: "138307". biodb.DEBUG[2025-10-05 21:39:10.617][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:10.619][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:10.632][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml. biodb.DEBUG[2025-10-05 21:39:10.633][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:10.635][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:10.640][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:10.646][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.673][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.675][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[2025-10-05 21:39:10.678][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.680][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.681][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.682][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.691][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.693][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.694][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.696][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.698][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.705][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.707][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.709][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.710][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.719][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.721][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.722][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.724][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.732][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.734][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.735][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.737][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.745][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.747][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.748][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.749][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.751][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.753][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.754][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.756][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.758][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.764][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.766][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.767][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.768][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:10.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.777][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.778][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.779][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.781][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:10.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:10.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.789][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.791][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.792][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.794][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.796][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:10.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:10.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.802][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:10.803][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:10.805][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.806][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:10.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:10.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:10.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.871][self$createEntryFromContent] Accession numbers: 138307. biodb.TRACE[2025-10-05 21:39:10.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:10.886][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.896][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:10.906][private$loadEntries] Creating entries from ids [1]: "176803". biodb.DEBUG[2025-10-05 21:39:10.907][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:10.909][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:10.917][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml. biodb.DEBUG[2025-10-05 21:39:10.919][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:10.920][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:10.922][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:10.924][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:10.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:10.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:10.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:10.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:10.933][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:10.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:10.937][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.939][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.940][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.941][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:10.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:10.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.947][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.949][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.950][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.951][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.953][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:10.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:10.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.957][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.959][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.960][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.961][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.962][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:10.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:10.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.967][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.969][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.970][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.971][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:10.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:10.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.977][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.979][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.980][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.981][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:10.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:10.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.987][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.988][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:10.989][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.991][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.992][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.993][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.994][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:10.995][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:10.997][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:10.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:10.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.002][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.003][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.004][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.005][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.012][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.013][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.014][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.015][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.021][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.022][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.024][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.025][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.026][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.031][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.032][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.033][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.034][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.087][self$createEntryFromContent] Accession numbers: 176803. biodb.TRACE[2025-10-05 21:39:11.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.109][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.119][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:11.121][private$loadEntries] Creating entries from ids [1]: "176962". biodb.DEBUG[2025-10-05 21:39:11.122][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:11.124][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:11.129][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml. biodb.DEBUG[2025-10-05 21:39:11.130][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:11.131][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:11.133][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:11.135][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.144][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:11.148][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.149][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.150][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.151][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.158][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:11.159][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:11.160][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.161][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.163][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:11.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:11.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.167][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:11.168][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:11.170][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.171][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:11.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:11.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.177][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:11.178][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:11.179][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.180][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:11.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:11.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.187][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:11.188][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:11.189][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.190][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:11.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:11.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.196][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:11.197][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:11.199][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.200][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.201][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:11.202][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.203][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.205][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.206][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:11.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.211][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.212][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.213][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.214][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.220][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.222][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.223][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.224][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.225][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.230][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.231][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.232][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.234][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.235][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.240][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.241][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.242][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.243][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.245][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.303][self$createEntryFromContent] Accession numbers: 176962. biodb.TRACE[2025-10-05 21:39:11.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.318][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.328][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:11.330][private$loadEntries] Creating entries from ids [1]: "198655". biodb.DEBUG[2025-10-05 21:39:11.331][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:11.333][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:11.341][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml. biodb.DEBUG[2025-10-05 21:39:11.343][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:11.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:11.346][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:11.349][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.362][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:11.367][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.369][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.370][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.372][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.380][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:11.382][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:11.383][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.384][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.386][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:11.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:11.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.393][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:11.395][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:11.396][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.398][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:11.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:11.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.406][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:11.408][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:11.410][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.411][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:11.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:11.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.419][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:11.421][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:11.423][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.424][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:11.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:11.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.432][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:11.434][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:11.436][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.437][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.439][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:11.441][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.442][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.443][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.445][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:11.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.452][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.453][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.455][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.456][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.464][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.466][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.467][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.469][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.477][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.478][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.480][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.481][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.483][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.489][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.490][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.491][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.493][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.563][self$createEntryFromContent] Accession numbers: 198655. biodb.TRACE[2025-10-05 21:39:11.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.581][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.593][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.595][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[2025-10-05 21:39:11.597][private$loadEntries] Creating entries from ids [1]: "215045". biodb.DEBUG[2025-10-05 21:39:11.598][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:11.601][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:11.610][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml. biodb.DEBUG[2025-10-05 21:39:11.612][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:11.614][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:11.616][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:11.619][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.631][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.632][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[2025-10-05 21:39:11.636][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.637][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.639][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.640][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.648][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:11.650][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:11.651][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.652][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.654][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:11.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:11.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.660][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:11.662][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:11.663][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.665][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.667][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:11.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:11.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.673][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:11.675][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:11.676][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.677][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:11.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:11.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.685][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:11.687][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:11.688][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.690][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:11.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:11.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.697][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:11.699][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:11.700][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.702][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.704][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:11.705][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.707][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.708][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.710][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:11.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.720][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.726][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.727][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.729][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:11.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.735][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.737][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.738][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.740][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.741][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:11.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:11.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.746][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.747][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.748][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.749][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.751][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:11.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:11.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.756][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.757][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.758][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.759][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.761][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:11.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:11.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:11.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:11.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:11.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.818][self$createEntryFromContent] Accession numbers: 215045. biodb.TRACE[2025-10-05 21:39:11.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:11.853][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:11.856][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:11.860][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:11.862][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:11.865][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.875][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:11.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.891][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.901][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:11.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.927][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.937][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:11.963][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:11.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:11.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:11.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:11.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:11.973][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:11.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:11.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:11.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:11.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:11.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.007][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.017][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.033][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.042][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.059][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.068][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.084][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.094][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.110][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.119][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.135][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.145][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.161][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.177][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.195][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.205][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.221][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.231][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.248][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.257][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.273][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.283][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.299][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.309][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.325][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.334][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.355][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.371][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.395][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.404][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.427][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.437][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:12.526][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:12.529][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:12.535][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/63dc67d905e130c19900bd338bad7ba9.content. sched.DEBUG[2025-10-05 21:39:12.536][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:12.544][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:12.551][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:12.558][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/287cac4c6e727656d926f26e3952924c.content. sched.DEBUG[2025-10-05 21:39:12.559][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:12.566][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.581][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:12.584][private$loadEntries] Creating entries from ids [1]: "4648". biodb.DEBUG[2025-10-05 21:39:12.585][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:12.587][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:12.599][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml. biodb.DEBUG[2025-10-05 21:39:12.600][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:12.605][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:12.606][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:12.608][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.627][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.630][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.632][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.633][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.634][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.640][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:12.641][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:12.642][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.643][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.645][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:12.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:12.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.650][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:12.651][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:12.652][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.653][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:12.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:12.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.659][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:12.661][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:12.662][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.663][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:12.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.669][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:12.670][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:12.671][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.673][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:12.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.682][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:12.683][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:12.684][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.688][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.690][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:12.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:12.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.703][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:12.704][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.705][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.706][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.708][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:12.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.713][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.714][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.715][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.716][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.722][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:12.724][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:12.725][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.726][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:12.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:12.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.733][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:12.734][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:12.735][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.736][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.738][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.743][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:12.744][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:12.745][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.746][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.748][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:12.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:12.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:12.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:12.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:12.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:12.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:12.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.801][self$createEntryFromContent] Accession numbers: 4648. biodb.TRACE[2025-10-05 21:39:12.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.827][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.850][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:12.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:12.870][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.883][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:12.886][private$loadEntries] Creating entries from ids [1]: "62447". biodb.DEBUG[2025-10-05 21:39:12.888][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:12.890][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:12.899][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml. biodb.DEBUG[2025-10-05 21:39:12.901][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:12.903][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:12.904][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:12.907][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:12.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:12.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:12.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:12.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:12.920][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:12.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:12.925][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.927][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.929][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.930][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:12.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:12.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.938][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:12.940][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:12.941][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.942][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.944][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:12.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:12.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.951][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:12.952][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:12.954][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.955][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:12.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:12.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.964][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:12.965][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:12.967][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.968][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:12.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:12.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.976][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:12.978][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:12.979][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.980][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:12.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:12.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.988][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:12.990][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:12.991][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.993][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:12.994][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:12.996][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:12.997][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:12.999][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.001][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:13.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:13.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.007][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.008][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.010][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.011][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.019][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:13.021][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:13.022][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.023][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:13.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:13.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.032][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:13.033][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:13.035][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.036][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.038][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:13.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:13.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.044][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:13.046][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:13.047][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.048][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.050][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:13.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:13.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:13.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:13.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:13.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:13.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:13.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:13.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:13.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:13.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:13.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:13.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:13.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:13.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:13.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:13.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:13.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:13.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:13.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:13.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:13.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:13.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.124][self$createEntryFromContent] Accession numbers: 62447. biodb.TRACE[2025-10-05 21:39:13.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:13.182][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:13.187][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:13.192][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:13.194][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:13.199][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.211][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.233][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.246][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.280][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.293][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.327][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.340][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.382][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.394][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.416][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.428][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.449][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.462][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.484][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.496][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.515][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.528][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.547][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.557][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.575][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.585][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.608][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.618][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.636][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.655][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.690][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.710][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.740][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.762][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.778][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.787][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.803][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.812][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.828][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.838][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.860][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.870][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.885][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.895][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:13.930][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:13.933][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:13.937][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content. sched.DEBUG[2025-10-05 21:39:13.938][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:13.942][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.951][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:13.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:13.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:13.983][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:13.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:13.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:13.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:13.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:13.996][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:13.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:13.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.022][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.031][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.063][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.073][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.098][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.107][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.123][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.132][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.148][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.157][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.173][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.182][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.198][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.208][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.224][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.233][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.256][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.265][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.281][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.290][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.307][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.316][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.332][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.341][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.357][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.367][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.385][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.395][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.416][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.427][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.458][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.470][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.490][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.502][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.522][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.534][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:14.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-10-05 21:39:14.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-10-05 21:39:14.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:14.590][biodb::testThat] biodb.INFO [2025-10-05 21:39:14.592][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2025-10-05 21:39:14.593][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:14.594][biodb::testThat] biodb.TRACE[2025-10-05 21:39:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-10-05 21:39:14.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-10-05 21:39:14.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.632][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.644][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:14.649][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:14.653][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:14.655][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content. sched.DEBUG[2025-10-05 21:39:14.657][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:14.660][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.672][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:14.702][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:14.706][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:14.709][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content. sched.DEBUG[2025-10-05 21:39:14.711][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:14.714][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.727][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.748][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.761][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:14.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:14.783][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-10-05 21:39:14.785][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.798][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.813][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.814][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:14.816][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:14.817][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:14.819][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.820][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.822][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.823][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.825][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.826][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.828][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.829][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.831][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.832][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.834][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.835][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.837][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.838][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.839][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.841][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:14.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.877][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2025-10-05 21:39:14.878][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.891][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.892][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[2025-10-05 21:39:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.905][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.907][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:14.908][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:14.909][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:14.911][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.912][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.914][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.915][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.916][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.918][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.919][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.921][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.922][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.923][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.924][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.926][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.927][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.936][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.937][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.939][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.958][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-10-05 21:39:14.959][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:14.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:14.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:14.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:14.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:14.970][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:14.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:14.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.985][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.986][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:14.987][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:14.988][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:14.990][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:14.991][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.993][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.994][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:14.995][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:14.997][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.998][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:14.999][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.001][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.002][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.004][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.005][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.006][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.008][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.009][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.011][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:15.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.029][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2025-10-05 21:39:15.031][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-10-05 21:39:15.032][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-10-05 21:39:15.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:15.169][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.180][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:15.185][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:15.189][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:15.195][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content. sched.DEBUG[2025-10-05 21:39:15.197][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:15.205][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:15.209][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:15.216][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content. sched.DEBUG[2025-10-05 21:39:15.218][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:15.221][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.233][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:15.254][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.266][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:15.287][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.300][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:15.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:15.361][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-10-05 21:39:15.408][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.421][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.436][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.437][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:15.439][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:15.440][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:15.442][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.443][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.445][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.446][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.448][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.449][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.451][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.452][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.454][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.455][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.457][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.458][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.460][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.461][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.462][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.464][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:15.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.484][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2025-10-05 21:39:15.485][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.498][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.570][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.572][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:15.573][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:15.575][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:15.576][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.578][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.579][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.581][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.582][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.584][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.585][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.587][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.588][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.590][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.607][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.609][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.610][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.612][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.613][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.615][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:15.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.642][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-10-05 21:39:15.644][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.655][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.670][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.671][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:15.672][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:15.673][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:15.675][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.676][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.678][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.679][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.681][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.682][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.684][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.685][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.686][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.688][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.689][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:15.691][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.692][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.694][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.695][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.697][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:15.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:15.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.717][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2025-10-05 21:39:15.718][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-10-05 21:39:15.720][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-10-05 21:39:15.732][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-10-05 21:39:15.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-10-05 21:39:15.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:15.743][biodb::testThat] biodb.INFO [2025-10-05 21:39:15.744][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2025-10-05 21:39:15.746][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:15.747][biodb::testThat] biodb.TRACE[2025-10-05 21:39:15.751][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-10-05 21:39:15.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-10-05 21:39:15.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:15.784][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.796][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:15.801][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:15.805][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:15.808][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content. sched.DEBUG[2025-10-05 21:39:15.809][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:15.813][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.825][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:15.847][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:15.851][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:15.854][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content. sched.DEBUG[2025-10-05 21:39:15.855][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:15.859][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:15.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:15.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:15.878][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:15.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:15.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:15.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:15.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:15.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:15.983][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:15.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:15.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.008][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:16.047][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-10-05 21:39:16.054][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.078][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.096][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.098][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:16.099][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:16.100][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:16.101][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.102][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.104][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.105][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.106][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.108][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.109][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.110][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.112][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.113][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.114][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.115][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.116][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.118][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.119][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.120][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:16.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.142][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2025-10-05 21:39:16.147][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.172][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.198][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.207][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:16.208][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:16.210][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:16.213][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.214][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.215][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.218][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.219][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.225][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.227][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.232][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.233][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.239][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.241][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.242][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.247][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.248][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.253][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.255][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:16.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.294][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-10-05 21:39:16.295][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.305][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.327][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.328][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:16.330][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:16.331][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:16.332][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.334][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.335][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.337][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.338][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.339][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.341][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.342][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.344][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.345][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.347][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.348][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.349][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.351][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.352][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.354][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:16.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.373][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2025-10-05 21:39:16.374][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-10-05 21:39:16.376][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-10-05 21:39:16.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:16.414][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.426][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:16.431][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:16.435][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:16.437][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content. sched.DEBUG[2025-10-05 21:39:16.439][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:16.443][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:16.446][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:16.450][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content. sched.DEBUG[2025-10-05 21:39:16.451][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:16.454][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.466][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:16.487][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.499][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:16.520][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.533][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:16.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:16.561][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-10-05 21:39:16.564][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.577][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.592][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.593][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:16.595][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:16.596][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:16.597][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.599][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.601][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.602][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.603][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.605][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.606][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.608][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.609][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.611][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.612][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.614][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.615][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.617][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.618][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.619][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:16.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.639][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2025-10-05 21:39:16.641][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.653][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.668][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.670][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:16.671][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:16.673][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:16.674][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.676][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.677][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.679][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.680][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.682][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.683][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.685][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.686][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.688][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.689][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.691][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.692][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.694][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.695][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.697][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:16.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.717][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-10-05 21:39:16.719][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.732][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.748][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.749][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:16.750][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:16.752][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:16.753][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.755][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.757][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.758][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.759][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.761][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.763][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.764][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.766][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.767][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.769][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:16.770][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.772][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.773][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.775][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.776][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:16.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:16.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.805][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2025-10-05 21:39:16.806][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-10-05 21:39:16.808][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-10-05 21:39:16.820][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-10-05 21:39:16.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-10-05 21:39:16.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:16.832][biodb::testThat] biodb.INFO [2025-10-05 21:39:16.833][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2025-10-05 21:39:16.835][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:16.836][biodb::testThat] biodb.TRACE[2025-10-05 21:39:16.840][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-10-05 21:39:16.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-10-05 21:39:16.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:16.878][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.891][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:16.896][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:16.900][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:16.903][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content. sched.DEBUG[2025-10-05 21:39:16.904][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:16.908][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.919][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. sched.DEBUG[2025-10-05 21:39:16.941][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:16.945][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:16.948][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content. sched.DEBUG[2025-10-05 21:39:16.949][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:16.953][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:16.965][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:16.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:16.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:16.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:16.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:16.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:16.987][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:16.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:16.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:16.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:16.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.000][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:17.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:17.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:17.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:17.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-10-05 21:39:17.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:17.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:17.021][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-10-05 21:39:17.024][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.037][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.063][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.064][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:17.066][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:17.067][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:17.068][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.070][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.071][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.073][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.074][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.076][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.077][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.079][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.080][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.081][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.083][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.084][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.086][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.087][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.088][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.090][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:17.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.110][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2025-10-05 21:39:17.111][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.124][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.139][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.140][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:17.142][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:17.143][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:17.144][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.146][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.148][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.149][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.150][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.152][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.153][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.155][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.156][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.158][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.159][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.161][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.162][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.164][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.165][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.166][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:17.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.186][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-10-05 21:39:17.188][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.200][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.215][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.216][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:17.218][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:17.219][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:17.220][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.222][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.223][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.225][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.226][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.228][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.229][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.231][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.232][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.233][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.235][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.236][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.238][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.239][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.241][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.242][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:17.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.262][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2025-10-05 21:39:17.263][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-10-05 21:39:17.265][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-10-05 21:39:17.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:17.329][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:17.347][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:17.351][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:17.354][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content. sched.DEBUG[2025-10-05 21:39:17.355][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:17.360][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:17.363][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:17.367][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content. sched.DEBUG[2025-10-05 21:39:17.368][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:17.372][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.385][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:17.406][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.419][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:17.440][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.449][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:17.463][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-10-05 21:39:17.464][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.473][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.485][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.486][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:17.487][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:17.489][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:17.490][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.491][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.492][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.493][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.494][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.495][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.497][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.498][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.499][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.500][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.509][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.510][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.512][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.513][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.514][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.515][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:17.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.531][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2025-10-05 21:39:17.532][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.541][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.553][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.554][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:17.556][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:17.557][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:17.558][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.559][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.560][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.561][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.562][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.563][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.565][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.566][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.567][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.568][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.569][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.570][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.571][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.572][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.574][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.575][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:17.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.590][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-10-05 21:39:17.591][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.601][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.612][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.613][private$selectFields] Fields type: <NULL> biodb.TRACE[2025-10-05 21:39:17.615][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-10-05 21:39:17.616][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-10-05 21:39:17.617][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.618][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.619][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.620][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.621][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.623][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.624][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.625][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.626][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.627][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.628][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-10-05 21:39:17.630][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.631][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.632][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.633][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.634][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-10-05 21:39:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.651][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2025-10-05 21:39:17.652][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-10-05 21:39:17.653][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-10-05 21:39:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-10-05 21:39:17.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-10-05 21:39:17.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:17.682][biodb::testThat] biodb.INFO [2025-10-05 21:39:17.683][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL "). biodb.INFO [2025-10-05 21:39:17.684][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:17.685][biodb::testThat] biodb.DEBUG[2025-10-05 21:39:17.691][private$loadEntries] Creating entries from ids [1]: "WRONGA". biodb.DEBUG[2025-10-05 21:39:17.699][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:17.701][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:17.707][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml. biodb.DEBUG[2025-10-05 21:39:17.709][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:17.714][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:17.715][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:17.719][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.736][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.746][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.747][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.748][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.749][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.755][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:17.756][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:17.758][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.759][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.760][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:17.761][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:17.762][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.764][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.765][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:17.766][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:17.767][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.769][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.770][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:17.771][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:17.772][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.773][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.779][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:17.780][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:17.781][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.782][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.784][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:17.785][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:17.786][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.787][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.789][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.790][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:17.791][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.792][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.794][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:17.795][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:17.796][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.797][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.798][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:17.800][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:17.801][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.802][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.803][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:17.804][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:17.806][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.807][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:17.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:17.855][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2025-10-05 21:39:17.856][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2025-10-05 21:39:17.865][biodb::testThat] biodb.INFO [2025-10-05 21:39:17.866][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones "). biodb.INFO [2025-10-05 21:39:17.867][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:17.868][biodb::testThat] biodb.DEBUG[2025-10-05 21:39:17.885][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799" biodb.DEBUG[2025-10-05 21:39:17.887][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799". biodb.DEBUG[2025-10-05 21:39:17.888][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)... fscache.INFO [2025-10-05 21:39:17.890][cch$loadContents] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:17.895][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml. fscache.DEBUG[2025-10-05 21:39:17.902][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml. fscache.DEBUG[2025-10-05 21:39:17.907][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml. biodb.DEBUG[2025-10-05 21:39:17.913][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:17.915][self$createEntryFromContent] Creating ChEBI entries from 3 content(s). biodb.DEBUG[2025-10-05 21:39:17.916][self$createEntryFromContent] Parsing 3 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:17.918][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:17.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:17.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:17.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:17.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:17.933][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:17.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:17.969][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.971][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.977][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.978][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:17.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:17.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.990][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:17.995][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:17.996][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:17.998][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:17.999][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:18.000][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:18.001][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.006][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.008][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:18.013][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:18.014][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.015][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.020][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:18.022][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:18.023][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.024][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.025][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.027][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.032][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.033][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.038][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:18.040][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:18.041][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.044][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.046][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.047][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.048][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.050][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.051][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:18.052][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:18.053][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.055][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.056][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:18.057][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:18.058][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.060][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.061][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:18.062][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:18.063][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.064][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:18.122][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:18.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:18.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:18.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:18.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:18.140][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:18.149][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.151][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.152][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.155][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.167][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:18.171][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:18.172][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.174][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.175][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:18.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:18.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.181][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:18.183][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:18.188][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.189][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:18.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:18.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.205][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:18.206][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:18.207][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.209][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:18.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:18.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.224][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:18.225][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:18.226][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.231][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:18.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:18.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.237][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.239][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.240][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.241][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.243][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.251][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:18.252][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:18.253][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.254][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:18.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:18.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.264][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.266][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.267][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.268][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.284][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:18.285][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:18.286][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.287][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:18.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:18.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.294][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:18.295][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:18.296][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.297][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.298][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:18.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:18.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.303][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:18.304][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:18.309][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.310][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.313][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:18.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:18.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:18.377][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:18.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:18.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:18.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:18.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:18.393][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:18.401][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.404][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.405][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.406][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.412][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:18.413][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:18.414][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.415][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.417][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:18.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:18.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.422][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:18.423][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:18.424][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.425][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.427][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:18.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:18.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.431][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:18.432][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:18.435][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.436][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.442][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.448][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:18.449][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:18.454][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.456][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:18.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:18.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.463][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.464][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.469][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.470][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.472][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:18.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.478][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:18.479][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:18.480][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.485][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.487][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:18.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:18.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.492][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.493][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.494][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.495][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.501][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:18.502][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:18.504][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.505][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:18.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.515][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:18.517][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:18.518][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.519][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:18.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:18.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.533][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:18.539][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:18.540][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.550][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:18.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:18.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:18.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:18.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:18.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:18.724][self$createEntryFromContent] Accession numbers: , 2528, 7799. biodb.DEBUG[2025-10-05 21:39:18.725][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2025-10-05 21:39:18.726][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>" biodb.INFO [2025-10-05 21:39:18.741][biodb::testThat] biodb.INFO [2025-10-05 21:39:18.742][biodb::testThat] Running test function test.peak.table (" The peak table is correct. "). biodb.INFO [2025-10-05 21:39:18.743][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:18.744][biodb::testThat] biodb.INFO [2025-10-05 21:39:18.771][biodb::testThat] biodb.INFO [2025-10-05 21:39:18.772][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. "). biodb.INFO [2025-10-05 21:39:18.773][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:18.774][biodb::testThat] biodb.INFO [2025-10-05 21:39:18.783][biodb::testThat] biodb.INFO [2025-10-05 21:39:18.784][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. "). biodb.INFO [2025-10-05 21:39:18.785][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:18.787][biodb::testThat] sched.DEBUG[2025-10-05 21:39:18.789][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:18.792][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:18.806][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/02ece1564def26723013d564c4071584.content. sched.DEBUG[2025-10-05 21:39:18.811][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.TRACE[2025-10-05 21:39:18.836][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:18.837][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:18.839][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.840][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:18.841][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.842][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:18.843][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:18.844][ef$get] fields variable is a list. biodb.INFO [2025-10-05 21:39:18.846][biodb::testThat] biodb.INFO [2025-10-05 21:39:18.847][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. "). biodb.INFO [2025-10-05 21:39:18.855][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:18.856][biodb::testThat] biodb.ERROR[2025-10-05 21:39:18.872][conn$annotateMzValues] No column named "mz" was found inside data frame. biodb.ERROR[2025-10-05 21:39:18.889][ef$checkIsDefined] Field(s) "foo" is/are not defined. biodb.INFO [2025-10-05 21:39:18.902][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-10-05 21:39:18.903][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-10-05 21:39:18.904][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-10-05 21:39:18.905][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:18.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:18.907][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:18.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:18.910][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-10-05 21:39:18.922][biodb::testContext] biodb.INFO [2025-10-05 21:39:18.923][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:18.924][biodb::testContext] Test context - Test conversions biodb.INFO [2025-10-05 21:39:18.925][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:18.926][biodb::testContext] biodb.INFO [2025-10-05 21:39:18.929][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:18.931][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2025-10-05 21:39:18.935][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:18.937][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-10-05 21:39:18.938][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-10-05 21:39:18.939][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.942][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-10-05 21:39:18.943][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-10-05 21:39:18.944][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.947][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-10-05 21:39:18.949][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-10-05 21:39:18.950][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.953][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-10-05 21:39:18.954][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-10-05 21:39:18.955][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-10-05 21:39:18.956][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.959][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-10-05 21:39:18.960][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-10-05 21:39:18.962][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-10-05 21:39:18.963][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.965][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.DEBUG[2025-10-05 21:39:18.966][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-10-05 21:39:18.967][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-10-05 21:39:18.968][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.971][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-10-05 21:39:18.972][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-10-05 21:39:18.973][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-10-05 21:39:18.974][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.978][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-10-05 21:39:18.979][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-10-05 21:39:18.980][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.983][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-10-05 21:39:18.984][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-10-05 21:39:18.985][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-10-05 21:39:18.986][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.989][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:18.990][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-10-05 21:39:18.992][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-10-05 21:39:18.993][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-10-05 21:39:18.994][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-10-05 21:39:18.995][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-10-05 21:39:18.996][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:18.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:18.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:18.999][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-10-05 21:39:19.000][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-10-05 21:39:19.001][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.005][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-10-05 21:39:19.006][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-10-05 21:39:19.007][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.010][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-10-05 21:39:19.011][self$set] Set key offline to FALSE. biodb.DEBUG[2025-10-05 21:39:19.012][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.014][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[2025-10-05 21:39:19.015][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-10-05 21:39:19.016][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-10-05 21:39:19.018][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-10-05 21:39:19.019][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.022][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:19.023][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-10-05 21:39:19.032][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-10-05 21:39:19.047][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.054][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-10-05 21:39:19.056][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-10-05 21:39:19.057][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-10-05 21:39:19.058][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.062][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-10-05 21:39:19.064][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.065][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-10-05 21:39:19.066][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.067][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:19.068][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.069][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:19.071][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.072][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:19.073][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:19.074][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:19.075][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.076][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-10-05 21:39:19.077][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:19.078][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.080][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.081][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:19.081][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:19.081][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:19.081][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:19.081][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:19.082][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:19.083][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.085][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:19.086][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.088][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:19.089][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.091][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:19.092][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:19.093][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.094][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.095][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-10-05 21:39:19.097][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.098][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:19.099][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.101][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:19.102][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.103][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:19.104][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:19.106][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:19.108][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:19.109][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.110][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-10-05 21:39:19.111][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:19.112][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.113][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.115][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:19.115][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:19.115][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:19.115][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:19.115][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:19.116][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:19.117][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.119][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:19.120][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.122][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:19.124][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.126][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:19.126][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:19.128][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.129][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.130][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-10-05 21:39:19.132][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.133][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-10-05 21:39:19.134][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.136][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:19.137][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.138][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:19.140][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.141][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:19.142][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:19.143][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:19.144][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.146][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-10-05 21:39:19.147][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:19.148][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.149][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.150][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.151][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:19.152][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.154][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:19.156][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.158][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:19.159][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.160][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:19.161][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:19.162][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.163][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.165][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-10-05 21:39:19.167][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.168][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:19.169][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.170][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:19.171][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.172][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:19.174][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:19.176][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:19.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:19.179][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.180][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-10-05 21:39:19.181][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:19.182][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.183][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.184][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.185][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:19.187][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.189][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:19.190][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:19.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:19.192][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:19.193][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.194][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:19.195][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:19.196][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.198][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:19.200][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:19.201][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.203][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.209][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.215][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.221][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.234][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.240][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.246][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.251][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.257][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.266][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.DEBUG[2025-10-05 21:39:19.268][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.282][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.290][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.DEBUG[2025-10-05 21:39:19.295][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.302][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.308][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.314][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.319][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[2025-10-05 21:39:19.325][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.334][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-10-05 21:39:19.336][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-10-05 21:39:19.338][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-10-05 21:39:19.340][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-10-05 21:39:19.342][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:19.344][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-10-05 21:39:19.347][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-10-05 21:39:19.349][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-10-05 21:39:19.351][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-10-05 21:39:19.353][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-10-05 21:39:19.355][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:19.357][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-10-05 21:39:19.359][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-10-05 21:39:19.365][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-10-05 21:39:19.367][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-10-05 21:39:19.376][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-10-05 21:39:19.378][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-10-05 21:39:19.382][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-10-05 21:39:19.388][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:19.390][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-10-05 21:39:19.393][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-10-05 21:39:19.398][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-10-05 21:39:19.403][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-10-05 21:39:19.408][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-10-05 21:39:19.410][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-10-05 21:39:19.412][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-10-05 21:39:19.417][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-10-05 21:39:19.423][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-10-05 21:39:19.425][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-10-05 21:39:19.427][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-10-05 21:39:19.429][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-10-05 21:39:19.431][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-10-05 21:39:19.433][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-10-05 21:39:19.435][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-10-05 21:39:19.436][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-10-05 21:39:19.438][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-10-05 21:39:19.440][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-10-05 21:39:19.442][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-10-05 21:39:19.444][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-10-05 21:39:19.446][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-10-05 21:39:19.448][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-10-05 21:39:19.449][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-10-05 21:39:19.451][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-10-05 21:39:19.453][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-10-05 21:39:19.455][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-10-05 21:39:19.457][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-10-05 21:39:19.458][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-10-05 21:39:19.460][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-10-05 21:39:19.462][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-10-05 21:39:19.464][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-10-05 21:39:19.466][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-10-05 21:39:19.468][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-10-05 21:39:19.470][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-10-05 21:39:19.472][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-10-05 21:39:19.474][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-10-05 21:39:19.476][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-10-05 21:39:19.478][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-10-05 21:39:19.480][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-10-05 21:39:19.482][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-10-05 21:39:19.485][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-10-05 21:39:19.487][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-10-05 21:39:19.489][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-10-05 21:39:19.491][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-10-05 21:39:19.493][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-10-05 21:39:19.495][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-10-05 21:39:19.504][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-10-05 21:39:19.506][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:19.509][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:19.511][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-10-05 21:39:19.513][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-10-05 21:39:19.515][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-10-05 21:39:19.517][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-10-05 21:39:19.519][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-10-05 21:39:19.521][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-10-05 21:39:19.523][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-10-05 21:39:19.525][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-10-05 21:39:19.527][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-10-05 21:39:19.529][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-10-05 21:39:19.531][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-10-05 21:39:19.533][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-10-05 21:39:19.535][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-10-05 21:39:19.537][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-10-05 21:39:19.539][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-10-05 21:39:19.541][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-10-05 21:39:19.544][initialize] This is biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:19.545][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:19.547][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.549][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.552][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.561][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.571][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.579][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.589][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.598][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.607][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.616][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.626][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.635][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.643][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[2025-10-05 21:39:19.644][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.654][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.663][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.672][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.680][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[2025-10-05 21:39:19.681][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.691][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:19.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:19.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:19.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:19.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:19.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:19.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:19.701][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml". biodb.DEBUG[2025-10-05 21:39:19.706][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-10-05 21:39:19.714][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:19.715][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-10-05 21:39:19.719][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.720][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:19.724][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:19.725][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:19.729][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.021][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-10-05 21:39:20.022][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-10-05 21:39:20.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:20.025][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.026][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-10-05 21:39:20.027][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-10-05 21:39:20.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-10-05 21:39:20.030][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.031][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:20.031][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:20.031][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:20.032][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-10-05 21:39:20.033][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.035][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:20.036][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.038][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:20.039][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-10-05 21:39:20.039][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-10-05 21:39:20.040][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:20.041][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:20.042][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.043][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-10-05 21:39:20.043][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-10-05 21:39:20.050][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:20.052][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:20.054][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-10-05 21:39:20.056][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:20.058][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:20.059][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:20.063][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-10-05 21:39:20.067][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-10-05 21:39:20.069][biodb::testThat] biodb.INFO [2025-10-05 21:39:20.070][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. "). biodb.INFO [2025-10-05 21:39:20.071][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:20.072][biodb::testThat] sched.DEBUG[2025-10-05 21:39:20.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". fscache.INFO [2025-10-05 21:39:20.082][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.089][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content. sched.DEBUG[2025-10-05 21:39:20.090][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:20.094][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". fscache.INFO [2025-10-05 21:39:20.097][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.103][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content. sched.DEBUG[2025-10-05 21:39:20.104][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.109][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.127][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.128][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". sched.DEBUG[2025-10-05 21:39:20.135][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". fscache.INFO [2025-10-05 21:39:20.137][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.143][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content. sched.DEBUG[2025-10-05 21:39:20.144][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.150][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.163][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.183][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.192][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:20.199][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". fscache.INFO [2025-10-05 21:39:20.202][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.204][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content. sched.DEBUG[2025-10-05 21:39:20.205][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.207][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.222][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:20.229][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". fscache.INFO [2025-10-05 21:39:20.236][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.241][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content. sched.DEBUG[2025-10-05 21:39:20.243][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.250][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.268][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.272][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.282][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.283][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". sched.DEBUG[2025-10-05 21:39:20.288][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". fscache.INFO [2025-10-05 21:39:20.292][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.294][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content. sched.DEBUG[2025-10-05 21:39:20.295][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.297][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.313][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:20.316][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". fscache.INFO [2025-10-05 21:39:20.320][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.323][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content. sched.DEBUG[2025-10-05 21:39:20.324][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.326][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.338][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.340][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". sched.DEBUG[2025-10-05 21:39:20.342][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". fscache.INFO [2025-10-05 21:39:20.346][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.353][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/d853ab8a48594978d76c30b86726648a.content. sched.DEBUG[2025-10-05 21:39:20.354][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.360][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.380][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-10-05 21:39:20.393][biodb::testThat] biodb.INFO [2025-10-05 21:39:20.395][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. "). biodb.INFO [2025-10-05 21:39:20.397][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:20.399][biodb::testThat] sched.DEBUG[2025-10-05 21:39:20.404][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". fscache.INFO [2025-10-05 21:39:20.409][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.417][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/aa56e28005d49da17591454624aabcd2.content. sched.DEBUG[2025-10-05 21:39:20.418][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.422][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.448][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". sched.DEBUG[2025-10-05 21:39:20.475][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". fscache.INFO [2025-10-05 21:39:20.482][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:20.489][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/c62078a064e3122e21e26c3428179396.content. sched.DEBUG[2025-10-05 21:39:20.490][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:20.495][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:20.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.504][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-10-05 21:39:20.511][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-10-05 21:39:20.512][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-10-05 21:39:20.513][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-10-05 21:39:20.514][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:20.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:20.516][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.518][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-10-05 21:39:20.523][biodb::testContext] biodb.INFO [2025-10-05 21:39:20.524][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:20.525][biodb::testContext] Test context - Test web services biodb.INFO [2025-10-05 21:39:20.526][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:20.527][biodb::testContext] biodb.INFO [2025-10-05 21:39:20.530][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:20.532][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2025-10-05 21:39:20.536][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:20.537][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-10-05 21:39:20.538][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-10-05 21:39:20.539][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.543][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-10-05 21:39:20.544][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-10-05 21:39:20.545][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.548][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-10-05 21:39:20.549][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-10-05 21:39:20.550][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.553][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-10-05 21:39:20.554][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-10-05 21:39:20.556][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-10-05 21:39:20.557][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.560][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-10-05 21:39:20.561][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-10-05 21:39:20.562][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-10-05 21:39:20.563][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.566][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-10-05 21:39:20.567][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-10-05 21:39:20.568][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.571][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-10-05 21:39:20.573][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-10-05 21:39:20.574][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-10-05 21:39:20.575][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.578][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-10-05 21:39:20.579][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-10-05 21:39:20.580][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.583][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-10-05 21:39:20.584][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-10-05 21:39:20.585][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-10-05 21:39:20.586][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.589][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:20.590][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-10-05 21:39:20.592][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-10-05 21:39:20.593][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-10-05 21:39:20.594][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-10-05 21:39:20.595][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-10-05 21:39:20.596][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.599][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-10-05 21:39:20.600][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-10-05 21:39:20.601][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.604][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-10-05 21:39:20.605][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-10-05 21:39:20.606][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.609][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-10-05 21:39:20.611][self$set] Set key offline to FALSE. biodb.DEBUG[2025-10-05 21:39:20.612][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.615][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-10-05 21:39:20.616][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-10-05 21:39:20.617][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-10-05 21:39:20.618][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.620][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[2025-10-05 21:39:20.621][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:20.622][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-10-05 21:39:20.630][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-10-05 21:39:20.631][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.634][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-10-05 21:39:20.635][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-10-05 21:39:20.636][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-10-05 21:39:20.637][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.640][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-10-05 21:39:20.642][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.644][self$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[2025-10-05 21:39:20.645][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.646][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:20.647][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.648][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:20.649][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.650][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:20.651][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:20.653][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:20.654][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.655][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-10-05 21:39:20.656][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:20.657][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.658][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.659][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:20.659][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:20.659][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:20.659][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:20.659][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:20.661][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:20.662][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.664][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:20.665][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.666][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.667][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:20.668][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.669][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:20.670][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:20.671][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.672][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.674][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-10-05 21:39:20.676][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.677][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:20.678][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.679][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:20.680][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.681][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:20.682][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.684][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:20.685][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:20.686][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:20.687][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.688][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-10-05 21:39:20.689][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:20.690][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.692][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.693][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:20.693][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:20.693][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:20.693][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:20.693][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:20.694][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:20.695][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.697][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:20.698][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.700][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:20.702][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.703][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:20.704][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:20.705][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.706][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.707][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-10-05 21:39:20.710][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.711][self$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[2025-10-05 21:39:20.712][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.713][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:20.714][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.716][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:20.717][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.722][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:20.723][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:20.724][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:20.725][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.727][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-10-05 21:39:20.731][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:20.732][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.733][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.738][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.739][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:20.740][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.747][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:20.749][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.751][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:20.756][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.757][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:20.759][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:20.764][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.765][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.770][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-10-05 21:39:20.775][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.776][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:20.777][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.782][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:20.784][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.788][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:20.789][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.790][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:20.795][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:20.797][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:20.799][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.800][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-10-05 21:39:20.801][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:20.806][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.808][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:20.813][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.814][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:20.815][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.822][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:20.827][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:20.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:20.830][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:20.831][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.832][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:20.833][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:20.835][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:20.836][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:20.838][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:20.839][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.840][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.DEBUG[2025-10-05 21:39:20.841][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.846][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[2025-10-05 21:39:20.847][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.852][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[2025-10-05 21:39:20.853][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.859][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.865][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.871][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.878][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.884][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.890][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.902][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.907][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.912][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.917][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.922][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.927][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.932][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:20.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:20.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:20.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:20.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:20.937][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-10-05 21:39:20.938][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-10-05 21:39:20.940][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-10-05 21:39:20.942][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-10-05 21:39:20.943][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:20.945][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-10-05 21:39:20.946][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-10-05 21:39:20.948][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-10-05 21:39:20.949][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-10-05 21:39:20.951][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-10-05 21:39:20.952][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:20.954][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-10-05 21:39:20.955][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-10-05 21:39:20.957][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-10-05 21:39:20.959][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-10-05 21:39:20.960][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-10-05 21:39:20.962][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-10-05 21:39:20.967][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-10-05 21:39:20.969][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:20.974][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-10-05 21:39:20.976][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-10-05 21:39:20.977][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-10-05 21:39:20.979][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-10-05 21:39:20.980][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-10-05 21:39:20.982][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-10-05 21:39:20.983][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-10-05 21:39:20.985][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-10-05 21:39:20.986][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-10-05 21:39:20.988][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-10-05 21:39:20.990][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-10-05 21:39:20.991][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-10-05 21:39:20.993][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-10-05 21:39:20.994][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-10-05 21:39:20.996][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-10-05 21:39:20.997][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-10-05 21:39:20.999][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-10-05 21:39:21.000][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-10-05 21:39:21.002][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-10-05 21:39:21.003][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-10-05 21:39:21.005][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-10-05 21:39:21.006][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-10-05 21:39:21.008][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-10-05 21:39:21.009][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-10-05 21:39:21.011][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-10-05 21:39:21.013][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-10-05 21:39:21.014][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-10-05 21:39:21.016][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-10-05 21:39:21.017][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-10-05 21:39:21.019][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-10-05 21:39:21.020][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-10-05 21:39:21.022][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-10-05 21:39:21.023][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-10-05 21:39:21.025][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-10-05 21:39:21.026][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-10-05 21:39:21.028][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-10-05 21:39:21.030][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-10-05 21:39:21.031][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-10-05 21:39:21.033][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-10-05 21:39:21.034][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-10-05 21:39:21.036][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-10-05 21:39:21.037][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-10-05 21:39:21.039][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-10-05 21:39:21.040][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-10-05 21:39:21.042][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-10-05 21:39:21.043][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-10-05 21:39:21.045][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-10-05 21:39:21.046][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:21.048][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:21.050][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-10-05 21:39:21.051][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-10-05 21:39:21.053][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-10-05 21:39:21.054][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-10-05 21:39:21.056][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-10-05 21:39:21.057][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-10-05 21:39:21.059][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-10-05 21:39:21.061][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-10-05 21:39:21.062][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-10-05 21:39:21.064][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-10-05 21:39:21.065][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-10-05 21:39:21.067][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-10-05 21:39:21.068][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-10-05 21:39:21.070][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-10-05 21:39:21.072][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-10-05 21:39:21.073][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-10-05 21:39:21.075][initialize] This is biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:21.076][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:21.077][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.079][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.080][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[2025-10-05 21:39:21.081][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.088][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.095][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.102][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.110][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.116][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[2025-10-05 21:39:21.117][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.124][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.131][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.139][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.146][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.158][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.169][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.176][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.182][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[2025-10-05 21:39:21.184][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.191][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.198][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.207][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml". biodb.DEBUG[2025-10-05 21:39:21.208][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-10-05 21:39:21.211][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.216][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-10-05 21:39:21.217][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.218][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:21.220][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.221][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:21.222][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.227][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-10-05 21:39:21.228][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-10-05 21:39:21.233][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:21.235][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.241][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-10-05 21:39:21.242][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-10-05 21:39:21.248][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-10-05 21:39:21.250][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.254][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:21.254][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:21.254][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:21.256][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-10-05 21:39:21.257][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.264][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:21.266][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.269][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:21.270][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-10-05 21:39:21.270][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-10-05 21:39:21.272][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:21.273][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:21.282][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.284][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-10-05 21:39:21.284][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-10-05 21:39:21.285][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:21.288][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:21.290][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-10-05 21:39:21.292][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:21.294][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:21.296][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:21.301][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-10-05 21:39:21.305][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-10-05 21:39:21.307][biodb::testThat] biodb.INFO [2025-10-05 21:39:21.308][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. "). biodb.INFO [2025-10-05 21:39:21.310][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:21.311][biodb::testThat] sched.DEBUG[2025-10-05 21:39:21.314][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". fscache.INFO [2025-10-05 21:39:21.318][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:21.326][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content. sched.DEBUG[2025-10-05 21:39:21.328][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:21.333][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL". fscache.INFO [2025-10-05 21:39:21.336][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:21.342][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/45b8073beb9f4a9f751edf98e80ca9dd.content. sched.DEBUG[2025-10-05 21:39:21.344][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.INFO [2025-10-05 21:39:21.358][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-10-05 21:39:21.360][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-10-05 21:39:21.361][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-10-05 21:39:21.363][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.365][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.368][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-10-05 21:39:21.374][biodb::testContext] biodb.INFO [2025-10-05 21:39:21.375][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:21.376][biodb::testContext] Test context - Non regression tests biodb.INFO [2025-10-05 21:39:21.378][biodb::testContext] ******************************************************************************** biodb.INFO [2025-10-05 21:39:21.379][biodb::testContext] biodb.INFO [2025-10-05 21:39:21.382][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:21.384][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2025-10-05 21:39:21.390][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:21.391][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-10-05 21:39:21.393][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-10-05 21:39:21.394][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.398][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-10-05 21:39:21.399][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-10-05 21:39:21.401][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.404][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-10-05 21:39:21.406][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-10-05 21:39:21.407][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.410][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[2025-10-05 21:39:21.411][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-10-05 21:39:21.412][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-10-05 21:39:21.414][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-10-05 21:39:21.415][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.419][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-10-05 21:39:21.420][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-10-05 21:39:21.422][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-10-05 21:39:21.423][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.427][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-10-05 21:39:21.428][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-10-05 21:39:21.429][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.433][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-10-05 21:39:21.435][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-10-05 21:39:21.436][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-10-05 21:39:21.438][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.441][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-10-05 21:39:21.443][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-10-05 21:39:21.444][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.448][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-10-05 21:39:21.450][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-10-05 21:39:21.451][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-10-05 21:39:21.452][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.456][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:21.458][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-10-05 21:39:21.459][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-10-05 21:39:21.461][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-10-05 21:39:21.462][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-10-05 21:39:21.464][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-10-05 21:39:21.465][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.469][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-10-05 21:39:21.470][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-10-05 21:39:21.472][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.474][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[2025-10-05 21:39:21.476][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-10-05 21:39:21.477][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-10-05 21:39:21.478][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.482][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-10-05 21:39:21.484][self$set] Set key offline to FALSE. biodb.DEBUG[2025-10-05 21:39:21.485][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.488][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[2025-10-05 21:39:21.489][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-10-05 21:39:21.490][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-10-05 21:39:21.492][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-10-05 21:39:21.493][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.497][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-10-05 21:39:21.499][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-10-05 21:39:21.512][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-10-05 21:39:21.513][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.519][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-10-05 21:39:21.520][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-10-05 21:39:21.526][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-10-05 21:39:21.527][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.534][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-10-05 21:39:21.540][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.541][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-10-05 21:39:21.546][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.548][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:21.549][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.550][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:21.551][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.556][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:21.557][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:21.558][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:21.559][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.561][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-10-05 21:39:21.562][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:21.563][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.564][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.565][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:21.565][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:21.565][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:21.565][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:21.565][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:21.566][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:21.567][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.569][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:21.571][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.573][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:21.574][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.575][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:21.576][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:21.577][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.578][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.580][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-10-05 21:39:21.582][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.583][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:21.584][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.585][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:21.586][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.588][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:21.589][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.590][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:21.591][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:21.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:21.594][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.595][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-10-05 21:39:21.596][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:21.597][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.598][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.600][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:21.600][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:21.600][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:21.600][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-10-05 21:39:21.600][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-10-05 21:39:21.601][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:21.602][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.604][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:21.605][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.607][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:21.608][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.609][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:21.610][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:21.612][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.613][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.614][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-10-05 21:39:21.616][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.618][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-10-05 21:39:21.619][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.620][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:21.621][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.622][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:21.624][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.625][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:21.626][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-10-05 21:39:21.627][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:21.628][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.630][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-10-05 21:39:21.631][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:21.632][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.633][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.634][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.636][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:21.637][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.639][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:21.640][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.642][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:21.643][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.644][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:21.645][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:21.647][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.648][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.649][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-10-05 21:39:21.651][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.653][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-10-05 21:39:21.654][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.655][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:21.656][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.657][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:21.659][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.660][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-10-05 21:39:21.661][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-10-05 21:39:21.662][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:21.663][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.664][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-10-05 21:39:21.666][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:21.667][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.668][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-10-05 21:39:21.669][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.670][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-10-05 21:39:21.672][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.674][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:21.675][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:21.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:21.677][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:21.678][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.679][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:21.681][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:21.682][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-10-05 21:39:21.683][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-10-05 21:39:21.685][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:21.686][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.688][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.693][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.697][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[2025-10-05 21:39:21.698][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.704][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.709][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.721][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.726][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.730][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.734][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[2025-10-05 21:39:21.735][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.740][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.745][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.750][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.754][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[2025-10-05 21:39:21.755][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.759][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[2025-10-05 21:39:21.760][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.765][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.770][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.775][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-10-05 21:39:21.777][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-10-05 21:39:21.778][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-10-05 21:39:21.780][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-10-05 21:39:21.782][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:21.783][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-10-05 21:39:21.785][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-10-05 21:39:21.786][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-10-05 21:39:21.788][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-10-05 21:39:21.789][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-10-05 21:39:21.791][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:21.792][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-10-05 21:39:21.794][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-10-05 21:39:21.795][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-10-05 21:39:21.797][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-10-05 21:39:21.798][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-10-05 21:39:21.800][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-10-05 21:39:21.801][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-10-05 21:39:21.803][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:21.804][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-10-05 21:39:21.806][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-10-05 21:39:21.808][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-10-05 21:39:21.809][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-10-05 21:39:21.811][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-10-05 21:39:21.812][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-10-05 21:39:21.814][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-10-05 21:39:21.815][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-10-05 21:39:21.817][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-10-05 21:39:21.818][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-10-05 21:39:21.820][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-10-05 21:39:21.821][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-10-05 21:39:21.823][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-10-05 21:39:21.824][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-10-05 21:39:21.826][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-10-05 21:39:21.827][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-10-05 21:39:21.829][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-10-05 21:39:21.831][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-10-05 21:39:21.832][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-10-05 21:39:21.834][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-10-05 21:39:21.835][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-10-05 21:39:21.837][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-10-05 21:39:21.838][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-10-05 21:39:21.840][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-10-05 21:39:21.841][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-10-05 21:39:21.843][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-10-05 21:39:21.844][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-10-05 21:39:21.846][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-10-05 21:39:21.847][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-10-05 21:39:21.849][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-10-05 21:39:21.851][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-10-05 21:39:21.852][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-10-05 21:39:21.854][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-10-05 21:39:21.855][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-10-05 21:39:21.857][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-10-05 21:39:21.858][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-10-05 21:39:21.860][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-10-05 21:39:21.862][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-10-05 21:39:21.863][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-10-05 21:39:21.865][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-10-05 21:39:21.866][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-10-05 21:39:21.868][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-10-05 21:39:21.870][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-10-05 21:39:21.871][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-10-05 21:39:21.873][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-10-05 21:39:21.874][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-10-05 21:39:21.876][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-10-05 21:39:21.878][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:21.879][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:21.881][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-10-05 21:39:21.882][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-10-05 21:39:21.884][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-10-05 21:39:21.885][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-10-05 21:39:21.887][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-10-05 21:39:21.889][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-10-05 21:39:21.890][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-10-05 21:39:21.892][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-10-05 21:39:21.893][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-10-05 21:39:21.895][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-10-05 21:39:21.896][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-10-05 21:39:21.898][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-10-05 21:39:21.900][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-10-05 21:39:21.901][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-10-05 21:39:21.903][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-10-05 21:39:21.904][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-10-05 21:39:21.906][initialize] This is biodb version 1.17.2. biodb.DEBUG[2025-10-05 21:39:21.907][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-10-05 21:39:21.908][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.911][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.913][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.920][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.927][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.934][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.942][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.948][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[2025-10-05 21:39:21.949][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.956][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.964][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.971][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.979][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.985][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[2025-10-05 21:39:21.986][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:21.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:21.994][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:21.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:21.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:21.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:21.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:21.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:22.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:22.001][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:22.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:22.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:22.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:22.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:22.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:22.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:22.009][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:22.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:22.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:22.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:22.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:22.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:22.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:22.016][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:22.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:22.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:22.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:22.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:22.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:22.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:22.024][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-10-05 21:39:22.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:22.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:22.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:22.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:22.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:22.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-10-05 21:39:22.032][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml". biodb.DEBUG[2025-10-05 21:39:22.034][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-10-05 21:39:22.036][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-10-05 21:39:22.037][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-10-05 21:39:22.046][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-10-05 21:39:22.047][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-10-05 21:39:22.048][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:22.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-10-05 21:39:22.050][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:22.051][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-10-05 21:39:22.052][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-10-05 21:39:22.053][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-10-05 21:39:22.054][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-10-05 21:39:22.056][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-10-05 21:39:22.057][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-10-05 21:39:22.058][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-10-05 21:39:22.059][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-10-05 21:39:22.060][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-10-05 21:39:22.060][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-10-05 21:39:22.060][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-10-05 21:39:22.061][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-10-05 21:39:22.062][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:22.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:22.064][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-10-05 21:39:22.066][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-10-05 21:39:22.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-10-05 21:39:22.068][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-10-05 21:39:22.069][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-10-05 21:39:22.069][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-10-05 21:39:22.070][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-10-05 21:39:22.071][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-10-05 21:39:22.072][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-10-05 21:39:22.073][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-10-05 21:39:22.073][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-10-05 21:39:22.074][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-10-05 21:39:22.076][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-10-05 21:39:22.078][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-10-05 21:39:22.079][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-10-05 21:39:22.081][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-10-05 21:39:22.083][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-10-05 21:39:22.087][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-10-05 21:39:22.090][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-10-05 21:39:22.092][biodb::testThat] biodb.INFO [2025-10-05 21:39:22.093][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. "). biodb.INFO [2025-10-05 21:39:22.094][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-10-05 21:39:22.095][biodb::testThat] sched.DEBUG[2025-10-05 21:39:22.097][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". fscache.INFO [2025-10-05 21:39:22.100][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:22.107][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content. sched.DEBUG[2025-10-05 21:39:22.108][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. sched.DEBUG[2025-10-05 21:39:22.112][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". fscache.INFO [2025-10-05 21:39:22.115][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched. fscache.DEBUG[2025-10-05 21:39:22.117][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/45b8073beb9f4a9f751edf98e80ca9dd.content. sched.DEBUG[2025-10-05 21:39:22.118][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache. biodb.DEBUG[2025-10-05 21:39:22.123][private$loadEntries] Creating entries from ids [1]: "2571". biodb.DEBUG[2025-10-05 21:39:22.125][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... fscache.INFO [2025-10-05 21:39:22.127][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. fscache.DEBUG[2025-10-05 21:39:22.147][FUN] Found encoding UTF-8 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml. biodb.DEBUG[2025-10-05 21:39:22.154][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-10-05 21:39:22.156][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-10-05 21:39:22.160][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-10-05 21:39:22.161][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-10-05 21:39:22.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:22.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:22.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:22.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:22.184][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:22.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-10-05 21:39:22.191][ef$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.193][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.194][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.196][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.203][ef$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:22.205][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:22.206][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.208][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.210][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-10-05 21:39:22.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-10-05 21:39:22.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.215][ef$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:22.217][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:22.218][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.220][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.222][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-10-05 21:39:22.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-10-05 21:39:22.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.227][ef$get] Asked field names are: inchi. biodb.TRACE[2025-10-05 21:39:22.229][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-10-05 21:39:22.230][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.231][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.234][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-10-05 21:39:22.235][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-10-05 21:39:22.236][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.238][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.240][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:22.241][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:22.243][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.244][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.246][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:22.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-10-05 21:39:22.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.252][ef$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:22.253][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:22.255][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.256][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.258][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-10-05 21:39:22.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-10-05 21:39:22.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.264][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:22.265][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:22.267][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.268][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:22.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-10-05 21:39:22.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.276][ef$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:22.278][ef$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:22.279][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.280][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-10-05 21:39:22.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-10-05 21:39:22.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.289][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:22.290][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:22.292][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.293][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.295][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-10-05 21:39:22.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-10-05 21:39:22.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.301][ef$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:22.302][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:22.304][ef$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.305][ef$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.307][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-10-05 21:39:22.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-10-05 21:39:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:22.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:22.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:22.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:22.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-10-05 21:39:22.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-10-05 21:39:22.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-10-05 21:39:22.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-10-05 21:39:22.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-10-05 21:39:22.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-10-05 21:39:22.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-10-05 21:39:22.413][self$createEntryFromContent] Accession numbers: 2571. biodb.INFO [2025-10-05 21:39:22.421][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-10-05 21:39:22.427][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-10-05 21:39:22.428][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-10-05 21:39:22.429][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-10-05 21:39:22.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-10-05 21:39:22.435][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-10-05 21:39:22.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-10-05 21:39:22.437][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-10-05 21:39:22.438][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". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 357 ] > > proc.time() user system elapsed 20.302 0.548 24.623
biodbChebi.Rcheck/biodbChebi-Ex.timings
name | user | system | elapsed | |
ChebiConn | 0.792 | 0.076 | 0.933 | |
ChebiEntry | 0.185 | 0.001 | 0.219 | |