Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-20 11:44 -0400 (Thu, 20 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
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 204/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: biodbChebi |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz |
StartedAt: 2025-03-19 18:26:24 -0400 (Wed, 19 Mar 2025) |
EndedAt: 2025-03-19 18:27:35 -0400 (Wed, 19 Mar 2025) |
EllapsedTime: 70.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbChebi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’ * using R Under development (unstable) (2025-03-02 r87868) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbChebi/DESCRIPTION’ ... OK * this is package ‘biodbChebi’ version ‘1.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbChebi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** this is package ‘biodbChebi’ version ‘1.13.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbChebi) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbChebi") biodb.INFO [2025-03-19 18:26:45.771][biodb::testContext] biodb.INFO [2025-03-19 18:26:45.773][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:26:45.773][biodb::testContext] Test context - Generic tests biodb.INFO [2025-03-19 18:26:45.773][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:26:45.773][biodb::testContext] biodb.INFO [2025-03-19 18:26:45.776][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:26:45.777][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-03-19 18:26:45.780][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:26:45.780][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-03-19 18:26:45.780][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-03-19 18:26:45.781][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.781][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-03-19 18:26:45.788][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-03-19 18:26:45.788][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.789][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-03-19 18:26:45.789][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-03-19 18:26:45.789][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.790][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-03-19 18:26:45.790][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-03-19 18:26:45.791][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-03-19 18:26:45.791][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.792][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-03-19 18:26:45.792][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-03-19 18:26:45.792][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-03-19 18:26:45.792][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.793][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-03-19 18:26:45.793][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-03-19 18:26:45.794][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.794][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-03-19 18:26:45.795][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-03-19 18:26:45.795][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-03-19 18:26:45.795][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.796][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-03-19 18:26:45.796][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-03-19 18:26:45.796][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.797][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-03-19 18:26:45.797][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-03-19 18:26:45.797][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-03-19 18:26:45.798][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.798][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:26:45.799][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-03-19 18:26:45.799][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-03-19 18:26:45.799][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-03-19 18:26:45.799][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-03-19 18:26:45.800][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-03-19 18:26:45.800][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.801][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-03-19 18:26:45.801][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-03-19 18:26:45.801][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.802][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-03-19 18:26:45.802][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-03-19 18:26:45.802][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.803][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-03-19 18:26:45.803][self$set] Set key offline to FALSE. biodb.DEBUG[2025-03-19 18:26:45.804][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.804][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-03-19 18:26:45.805][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-03-19 18:26:45.805][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.806][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-03-19 18:26:45.806][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-03-19 18:26:45.806][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.807][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:26:45.807][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-03-19 18:26:45.815][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-03-19 18:26:45.815][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.816][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[2025-03-19 18:26:45.816][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-03-19 18:26:45.817][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-03-19 18:26:45.817][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-03-19 18:26:45.817][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.819][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-03-19 18:26:45.831][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.838][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-03-19 18:26:45.839][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.839][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:26:45.839][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:26:45.840][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.840][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:26:45.844][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:26:45.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:26:45.845][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.845][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:26:45.846][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:26:45.847][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:26:45.847][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.848][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:26:45.848][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.848][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:26:45.849][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.849][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:26:45.849][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:26:45.849][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.850][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.850][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-03-19 18:26:45.850][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.851][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:26:45.851][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.851][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:26:45.851][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.852][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:26:45.852][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.852][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:26:45.852][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:26:45.853][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:26:45.853][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.853][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-03-19 18:26:45.853][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:26:45.854][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:26:45.855][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.855][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:26:45.855][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.856][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:26:45.857][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.857][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:26:45.857][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:26:45.857][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.858][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.858][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-03-19 18:26:45.858][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.859][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-03-19 18:26:45.859][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.859][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:26:45.859][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.860][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:26:45.860][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.860][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:26:45.860][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:26:45.861][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:26:45.861][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.861][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-03-19 18:26:45.861][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:26:45.862][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.862][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.862][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.862][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:26:45.863][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.863][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:26:45.863][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.864][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:26:45.864][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.864][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:26:45.864][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:26:45.865][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.865][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.865][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-03-19 18:26:45.866][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.866][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:26:45.866][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.867][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:26:45.867][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:26:45.867][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.868][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:26:45.868][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:26:45.868][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:26:45.868][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.868][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-03-19 18:26:45.869][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:26:45.869][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.869][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.869][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.870][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:26:45.870][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.870][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:26:45.871][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.871][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.871][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:26:45.871][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.872][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:26:45.872][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:26:45.872][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.872][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:26:45.874][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:26:45.874][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.874][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.876][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.877][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.878][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.879][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.880][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.881][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.882][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[2025-03-19 18:26:45.882][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.883][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.885][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.885][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[2025-03-19 18:26:45.886][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.889][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.890][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.891][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.892][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.894][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.895][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[2025-03-19 18:26:45.895][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.896][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.DEBUG[2025-03-19 18:26:45.896][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-03-19 18:26:45.898][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-03-19 18:26:45.898][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-03-19 18:26:45.899][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-03-19 18:26:45.899][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:26:45.900][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-03-19 18:26:45.900][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-03-19 18:26:45.900][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-03-19 18:26:45.901][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-03-19 18:26:45.901][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-03-19 18:26:45.901][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:26:45.902][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-03-19 18:26:45.902][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-03-19 18:26:45.903][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-03-19 18:26:45.903][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-03-19 18:26:45.903][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-03-19 18:26:45.904][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-03-19 18:26:45.904][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-03-19 18:26:45.904][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:26:45.905][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-03-19 18:26:45.905][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-03-19 18:26:45.906][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-03-19 18:26:45.906][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-03-19 18:26:45.906][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-03-19 18:26:45.907][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-03-19 18:26:45.907][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-03-19 18:26:45.907][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-03-19 18:26:45.908][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-03-19 18:26:45.908][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-03-19 18:26:45.909][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-03-19 18:26:45.909][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-03-19 18:26:45.909][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-03-19 18:26:45.910][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-03-19 18:26:45.910][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-03-19 18:26:45.910][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-03-19 18:26:45.911][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-03-19 18:26:45.911][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-03-19 18:26:45.911][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-03-19 18:26:45.912][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-03-19 18:26:45.912][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-03-19 18:26:45.913][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-03-19 18:26:45.913][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-03-19 18:26:45.913][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-03-19 18:26:45.914][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-03-19 18:26:45.914][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-03-19 18:26:45.914][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-03-19 18:26:45.915][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-03-19 18:26:45.915][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-03-19 18:26:45.915][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-03-19 18:26:45.916][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-03-19 18:26:45.916][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-03-19 18:26:45.916][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-03-19 18:26:45.917][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-03-19 18:26:45.917][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-03-19 18:26:45.918][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-03-19 18:26:45.918][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-03-19 18:26:45.918][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-03-19 18:26:45.919][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-03-19 18:26:45.919][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-03-19 18:26:45.919][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-03-19 18:26:45.920][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-03-19 18:26:45.920][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-03-19 18:26:45.920][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-03-19 18:26:45.921][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-03-19 18:26:45.921][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-03-19 18:26:45.922][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-03-19 18:26:45.922][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:26:45.922][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:26:45.923][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-03-19 18:26:45.923][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-03-19 18:26:45.923][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-03-19 18:26:45.924][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-03-19 18:26:45.924][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-03-19 18:26:45.924][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-03-19 18:26:45.925][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-03-19 18:26:45.925][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-03-19 18:26:45.926][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-03-19 18:26:45.926][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-03-19 18:26:45.926][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-03-19 18:26:45.927][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-03-19 18:26:45.927][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-03-19 18:26:45.927][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-03-19 18:26:45.928][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-03-19 18:26:45.930][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-03-19 18:26:45.930][initialize] This is biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:26:45.932][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:26:45.932][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.932][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.933][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[2025-03-19 18:26:45.934][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.936][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[2025-03-19 18:26:45.936][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.941][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[2025-03-19 18:26:45.941][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.943][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.944][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.946][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[2025-03-19 18:26:45.946][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.948][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.949][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.951][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.952][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[2025-03-19 18:26:45.953][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.954][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.956][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.957][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[2025-03-19 18:26:45.958][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.959][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.961][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.962][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:45.964][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:26:45.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:45.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:45.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:45.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:45.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:45.965][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[2025-03-19 18:26:45.966][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml". biodb.DEBUG[2025-03-19 18:26:45.969][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-03-19 18:26:45.970][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.970][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-03-19 18:26:45.970][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.971][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:26:45.971][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.971][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:26:45.971][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.972][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-03-19 18:26:45.972][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-03-19 18:26:45.972][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:26:45.972][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-03-19 18:26:45.973][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-03-19 18:26:45.974][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:26:45.974][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:26:45.974][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:26:45.974][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-03-19 18:26:45.974][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.975][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:26:45.975][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:26:45.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:26:45.975][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:26:45.976][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:45.976][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-03-19 18:26:45.976][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:26:45.976][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:26:45.976][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-03-19 18:26:45.977][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-03-19 18:26:45.977][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-03-19 18:26:45.979][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:26:45.979][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:26:45.980][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-03-19 18:26:45.980][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:26:45.980][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:26:45.981][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:26:45.991][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-03-19 18:26:45.991][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2025-03-19 18:26:45.993][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2025-03-19 18:26:45.995][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2025-03-19 18:26:46.014][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:26:46.015][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:26:46.015][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2025-03-19 18:26:46.016][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-03-19 18:26:46.019][biodb::testThat] biodb.INFO [2025-03-19 18:26:46.020][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2025-03-19 18:26:46.020][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:46.020][biodb::testThat] biodb.TRACE[2025-03-19 18:26:46.022][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml". biodb.DEBUG[2025-03-19 18:26:46.022][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:46.023][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:46.027][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:46.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:46.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:46.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:46.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:46.033][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:46.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:46.036][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.037][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.037][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.037][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.043][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.043][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.043][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.043][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.051][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.052][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.052][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.052][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.052][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.054][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.054][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.054][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.054][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.056][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.056][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.056][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.056][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.058][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.058][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.058][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.058][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.059][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.060][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:46.060][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.060][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.060][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.061][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:46.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.062][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.062][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.062][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.062][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.063][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.064][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.064][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.064][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.069][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:46.069][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.069][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.069][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.070][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:46.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.071][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.071][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.071][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.071][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.072][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:46.091][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440. biodb.TRACE[2025-03-19 18:26:46.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.106][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-03-19 18:26:46.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-03-19 18:26:46.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-03-19 18:26:46.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-03-19 18:26:46.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.108][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-03-19 18:26:46.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-03-19 18:26:46.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.109][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-03-19 18:26:46.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-03-19 18:26:46.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.139][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.139][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.140][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.140][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.148][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.149][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.149][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.149][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.156][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.156][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.156][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.156][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.162][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.163][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.163][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.163][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.163][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.170][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.170][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.170][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.170][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.177][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.177][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.177][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.177][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.181][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.182][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.183][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.184][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.184][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.184][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.184][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.187][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.190][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-03-19 18:26:46.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.191][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-03-19 18:26:46.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.192][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-03-19 18:26:46.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.193][ef$get] Asked field names are: n.stars. biodb.TRACE[2025-03-19 18:26:46.193][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.193][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.193][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.194][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2025-03-19 18:26:46.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.197][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.198][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.199][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.200][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.200][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.200][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.200][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.201][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.204][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.206][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.207][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.207][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.207][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.207][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.208][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.213][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.214][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.214][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.214][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.220][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.221][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.221][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.221][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.226][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.227][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.227][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.227][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.229][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.229][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.229][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.229][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.231][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.231][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.231][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.231][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.233][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.233][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.233][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.234][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.235][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.235][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.235][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.236][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.237][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.237][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.237][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.238][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.239][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.239][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.239][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.240][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.241][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.241][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.241][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.242][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.243][ef$get] Asked field names are: n.stars. biodb.TRACE[2025-03-19 18:26:46.243][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.243][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.244][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.245][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.245][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.245][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.246][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.247][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.247][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.247][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.248][ef$get] fields variable is a list. biodb.INFO [2025-03-19 18:26:46.250][biodb::testThat] biodb.INFO [2025-03-19 18:26:46.250][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2025-03-19 18:26:46.251][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:46.251][biodb::testThat] biodb.DEBUG[2025-03-19 18:26:46.255][private$loadEntries] Creating entries from ids [1]: "15440". biodb.DEBUG[2025-03-19 18:26:46.258][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:46.259][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440". biodb.TRACE[2025-03-19 18:26:46.259][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:26:46.260][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml". biodb.DEBUG[2025-03-19 18:26:46.260][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:46.269][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:46.269][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:46.270][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:46.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:46.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:46.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:46.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:46.273][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:46.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:46.274][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.274][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.274][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.274][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.280][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.281][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.281][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.281][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.282][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:46.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:46.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.283][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.283][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.283][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.283][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:46.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:46.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.284][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.285][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.285][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.285][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:46.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:46.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.286][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.287][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.287][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.287][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:46.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:46.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.288][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.288][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.289][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.289][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.289][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:46.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.290][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:46.290][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.291][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.291][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.291][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:46.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:46.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.292][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.292][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.292][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.293][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:46.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.294][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.294][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.294][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.295][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.296][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:46.296][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.296][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.297][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:46.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:46.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.298][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.298][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.298][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.298][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:46.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:46.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:46.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:46.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:46.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:46.311][self$createEntryFromContent] Accession numbers: 15440. biodb.TRACE[2025-03-19 18:26:46.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2025-03-19 18:26:46.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2025-03-19 18:26:46.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2025-03-19 18:26:46.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2025-03-19 18:26:46.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2025-03-19 18:26:46.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2025-03-19 18:26:46.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-03-19 18:26:46.317][biodb::testThat] biodb.INFO [2025-03-19 18:26:46.317][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2025-03-19 18:26:46.317][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:46.317][biodb::testThat] biodb.TRACE[2025-03-19 18:26:46.318][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.318][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.319][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.319][ef$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:46.319][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name". biodb.TRACE[2025-03-19 18:26:46.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:46.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:46.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:46.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:46.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:46.330][function(conn, opt)] With value "squalene". biodb.DEBUG[2025-03-19 18:26:46.332][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2025-03-19 18:26:46.338][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:26:46.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2025-03-19 18:26:46.345][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:26:46.345][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2025-03-19 18:26:46.352][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:26:46.353][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:46.353][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:46.354][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:26:46.894][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:26:47.415][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:47.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content" biodb.TRACE[2025-03-19 18:26:47.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request" biodb.DEBUG[2025-03-19 18:26:47.421][function(conn, opt)] With found IDs [1]: "15440". biodb.TRACE[2025-03-19 18:26:47.425][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:47.425][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:47.426][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.426][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.426][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.426][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.427][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.427][ef$get] fields variable is a list. biodb.INFO [2025-03-19 18:26:47.428][biodb::testThat] biodb.INFO [2025-03-19 18:26:47.428][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2025-03-19 18:26:47.429][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:47.429][biodb::testThat] biodb.TRACE[2025-03-19 18:26:47.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:47.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:47.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:47.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:47.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:47.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:47.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:47.458][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:26:47.459][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:26:47.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2025-03-19 18:26:47.460][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:26:47.461][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.INFO [2025-03-19 18:26:47.466][biodb::testThat] biodb.INFO [2025-03-19 18:26:47.466][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2025-03-19 18:26:47.467][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:47.467][biodb::testThat] biodb.TRACE[2025-03-19 18:26:47.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:47.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:47.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:47.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:47.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:47.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:47.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:47.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.483][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-03-19 18:26:47.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-03-19 18:26:47.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-03-19 18:26:47.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-03-19 18:26:47.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:47.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:47.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:47.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:47.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:47.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:47.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:47.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:47.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:47.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.495][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.496][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-03-19 18:26:47.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.497][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-03-19 18:26:47.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-03-19 18:26:47.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:47.498][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-03-19 18:26:47.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-03-19 18:26:47.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:47.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-03-19 18:26:47.503][biodb::testThat] biodb.INFO [2025-03-19 18:26:47.504][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2025-03-19 18:26:47.504][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:47.504][biodb::testThat] biodb.INFO [2025-03-19 18:26:47.507][biodb::testThat] biodb.INFO [2025-03-19 18:26:47.507][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2025-03-19 18:26:47.507][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:47.507][biodb::testThat] biodb.INFO [2025-03-19 18:26:47.510][biodb::testThat] biodb.INFO [2025-03-19 18:26:47.510][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2025-03-19 18:26:47.510][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:47.511][biodb::testThat] biodb.DEBUG[2025-03-19 18:26:47.512][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440". biodb.DEBUG[2025-03-19 18:26:48.435][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440. biodb.INFO [2025-03-19 18:26:49.641][biodb::testThat] biodb.INFO [2025-03-19 18:26:49.642][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2025-03-19 18:26:49.642][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:49.642][biodb::testThat] biodb.DEBUG[2025-03-19 18:26:50.033][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400. biodb.TRACE[2025-03-19 18:26:50.435][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:50.435][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:50.436][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.436][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.436][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:50.437][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:50.437][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.437][ef$get] fields variable is a list. biodb.INFO [2025-03-19 18:26:50.438][biodb::testThat] biodb.INFO [2025-03-19 18:26:50.438][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2025-03-19 18:26:50.439][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:26:50.439][biodb::testThat] biodb.TRACE[2025-03-19 18:26:50.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:50.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:50.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:50.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:50.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:50.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:50.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:50.477][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:26:50.478][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:26:50.478][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2025-03-19 18:26:50.479][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:26:50.479][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2025-03-19 18:26:50.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:26:50.507][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:26:50.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2025-03-19 18:26:50.508][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:26:50.508][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.TRACE[2025-03-19 18:26:50.513][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-03-19 18:26:50.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-03-19 18:26:50.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:50.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:50.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:50.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:50.525][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:26:50.530][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:50.530][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:50.535][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:26:50.896][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:26:51.711][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:51.712][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content" biodb.TRACE[2025-03-19 18:26:51.713][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request" biodb.DEBUG[2025-03-19 18:26:51.714][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:51.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:51.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:51.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:51.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:51.717][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:51.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:51.717][private$loadEntries] Creating entries from ids [1]: "192288". biodb.DEBUG[2025-03-19 18:26:51.734][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:51.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288". biodb.TRACE[2025-03-19 18:26:51.735][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:51.735][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:51.735][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:51.735][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:51.736][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:51.736][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:51.737][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:51.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:51.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:51.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:51.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:51.739][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:51.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:51.740][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288". biodb.DEBUG[2025-03-19 18:26:51.741][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:51.741][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:51.741][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288". biodb.TRACE[2025-03-19 18:26:52.176][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288). biodb.DEBUG[2025-03-19 18:26:52.564][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:52.565][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content" biodb.TRACE[2025-03-19 18:26:52.566][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request" biodb.TRACE[2025-03-19 18:26:52.567][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml" biodb.DEBUG[2025-03-19 18:26:52.567][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:52.568][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:52.568][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:52.569][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:52.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:52.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:52.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:52.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:52.572][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:52.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:52.573][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.573][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.573][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.574][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.577][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:52.579][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:52.579][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.579][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.580][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:52.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:52.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.581][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:52.581][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:52.581][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.582][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:52.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:52.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.583][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:52.584][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:52.584][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.584][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:52.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:52.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.586][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:52.586][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:52.586][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.586][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:52.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:52.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.588][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:52.588][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:52.588][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.589][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.589][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:52.589][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.589][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.590][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.590][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:52.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.591][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:52.591][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:52.592][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.592][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:52.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:52.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.593][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:52.593][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:52.594][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.594][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:52.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:52.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.595][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:52.596][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:52.596][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.596][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.596][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:52.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:52.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.597][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:52.598][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:52.598][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.598][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:52.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:52.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:52.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:52.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:52.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:52.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:52.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:52.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:52.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:52.612][self$createEntryFromContent] Accession numbers: 192288. biodb.TRACE[2025-03-19 18:26:52.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:52.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:52.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:52.619][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:26:52.620][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:52.620][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:52.621][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:26:52.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:26:53.346][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:53.347][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content" biodb.TRACE[2025-03-19 18:26:53.348][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request" biodb.DEBUG[2025-03-19 18:26:53.353][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:53.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:53.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:53.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:53.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:53.356][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:53.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:53.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:53.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:53.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:53.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:53.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:53.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:53.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:53.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:53.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:53.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:53.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:53.363][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:53.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:53.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:53.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:53.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:53.365][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:53.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:53.366][private$loadEntries] Creating entries from ids [1]: "209892". biodb.DEBUG[2025-03-19 18:26:53.366][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:53.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892". biodb.TRACE[2025-03-19 18:26:53.367][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:53.367][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:53.367][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:53.368][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:53.368][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:53.368][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:53.372][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:53.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:53.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:53.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:53.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:53.374][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:53.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:53.375][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892". biodb.DEBUG[2025-03-19 18:26:53.376][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:53.376][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:53.376][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892". biodb.TRACE[2025-03-19 18:26:53.981][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892). biodb.DEBUG[2025-03-19 18:26:54.326][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:54.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content" biodb.TRACE[2025-03-19 18:26:54.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request" biodb.TRACE[2025-03-19 18:26:54.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml" biodb.DEBUG[2025-03-19 18:26:54.330][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:54.330][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:54.331][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:54.331][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:54.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:54.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:54.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:54.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:54.334][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:54.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:54.335][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.335][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.336][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.336][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.341][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:54.341][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:54.341][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.341][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.342][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:54.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:54.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.343][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:54.343][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:54.344][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.344][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.344][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:54.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:54.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.346][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:54.346][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:54.346][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.346][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:54.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:54.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.348][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:54.348][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:54.348][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.349][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:54.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:54.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.350][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:54.350][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:54.351][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.351][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.351][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:54.351][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.352][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.352][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.352][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:54.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.353][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:54.354][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:54.354][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.354][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:54.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:54.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.355][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:54.356][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:54.356][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.356][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:54.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:54.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.358][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:54.358][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:54.358][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.358][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.359][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:54.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:54.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.360][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:54.360][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:54.360][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.361][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.361][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:54.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:54.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:54.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:54.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:54.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:54.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:54.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:54.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:54.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:54.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:54.388][self$createEntryFromContent] Accession numbers: 209892. biodb.TRACE[2025-03-19 18:26:54.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:54.398][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:26:54.400][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:26:54.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2025-03-19 18:26:54.400][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:26:54.401][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2025-03-19 18:26:54.402][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:54.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:54.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:54.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:54.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:54.404][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:54.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:54.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:54.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:54.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:54.408][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:54.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:54.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:54.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:54.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:54.411][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:54.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:54.411][private$loadEntries] Creating entries from ids [1]: "26747". biodb.DEBUG[2025-03-19 18:26:54.412][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:54.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747". biodb.TRACE[2025-03-19 18:26:54.415][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:54.416][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:54.416][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:54.416][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:54.417][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:54.417][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:54.418][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:54.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:54.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:54.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:54.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:54.421][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:54.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:54.421][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747". biodb.DEBUG[2025-03-19 18:26:54.422][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:54.423][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:54.423][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747". biodb.TRACE[2025-03-19 18:26:54.783][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747). biodb.DEBUG[2025-03-19 18:26:55.133][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:55.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content" biodb.TRACE[2025-03-19 18:26:55.135][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request" biodb.TRACE[2025-03-19 18:26:55.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml" biodb.DEBUG[2025-03-19 18:26:55.136][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:55.136][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:55.137][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:55.137][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:55.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:55.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:55.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:55.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:55.140][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:55.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:55.141][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.142][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.142][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.142][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.144][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:55.144][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:55.144][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.145][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.145][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:55.145][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:55.145][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.146][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.146][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:55.146][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:55.146][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.147][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.147][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:55.147][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:55.147][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.148][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.148][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:55.148][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:55.148][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.149][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.149][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:55.149][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.149][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.150][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.150][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:55.150][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:55.150][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.151][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.151][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:55.151][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:55.151][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.152][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.153][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:55.153][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:55.156][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.157][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:55.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.158][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:55.159][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:55.159][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.159][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:55.169][self$createEntryFromContent] Accession numbers: 26747. biodb.TRACE[2025-03-19 18:26:55.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:55.174][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:55.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:55.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:55.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:55.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:55.177][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:55.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:55.177][private$loadEntries] Creating entries from ids [1]: "59285". biodb.DEBUG[2025-03-19 18:26:55.178][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:55.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285". biodb.TRACE[2025-03-19 18:26:55.178][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:55.179][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:55.179][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:55.179][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:55.179][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:55.180][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:55.180][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:55.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:55.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:55.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:55.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:55.185][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:55.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:55.186][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285". biodb.DEBUG[2025-03-19 18:26:55.187][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:55.187][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:55.187][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285". biodb.TRACE[2025-03-19 18:26:55.577][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285). biodb.DEBUG[2025-03-19 18:26:55.934][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:55.935][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content" biodb.TRACE[2025-03-19 18:26:55.936][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request" biodb.TRACE[2025-03-19 18:26:55.937][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml" biodb.DEBUG[2025-03-19 18:26:55.938][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:55.938][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:55.939][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:55.939][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:55.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:55.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:55.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:55.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:55.942][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:55.942][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[2025-03-19 18:26:55.944][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.944][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.944][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.944][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.946][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:55.946][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:55.946][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.947][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.947][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:55.947][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:55.948][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.948][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.948][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:55.949][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:55.949][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.949][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.949][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:55.950][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:55.950][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.950][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.950][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:55.951][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:55.951][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.951][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.952][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:55.952][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.952][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.952][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.953][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:55.953][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:55.953][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.953][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.954][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:55.954][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:55.954][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.954][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:55.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:55.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.956][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:55.956][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:55.957][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.957][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.957][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:55.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:55.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.958][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:55.959][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:55.959][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.959][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:55.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:55.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:55.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:55.974][self$createEntryFromContent] Accession numbers: 59285. biodb.TRACE[2025-03-19 18:26:55.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:55.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:55.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:55.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:55.981][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:55.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:55.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:55.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:55.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:55.984][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:55.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:55.985][private$loadEntries] Creating entries from ids [1]: "75174". biodb.DEBUG[2025-03-19 18:26:55.985][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:55.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174". biodb.TRACE[2025-03-19 18:26:55.986][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:55.986][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:55.986][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:55.987][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:55.987][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:55.987][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:55.988][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:55.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:55.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:55.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:55.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:55.991][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:55.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:55.991][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174". biodb.DEBUG[2025-03-19 18:26:55.992][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:55.992][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:55.995][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174". biodb.TRACE[2025-03-19 18:26:56.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174). biodb.DEBUG[2025-03-19 18:26:57.063][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:57.064][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content" biodb.TRACE[2025-03-19 18:26:57.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request" biodb.TRACE[2025-03-19 18:26:57.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml" biodb.DEBUG[2025-03-19 18:26:57.067][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:57.067][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:57.068][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:57.068][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:57.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:57.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:57.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:57.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:57.071][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:57.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:57.072][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.073][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.073][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.073][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.075][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:57.075][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:57.075][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.075][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.076][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:57.076][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:57.076][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.076][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.077][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:57.077][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:57.077][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.078][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.078][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:57.078][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:57.078][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.079][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.079][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:57.079][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:57.080][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.080][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.080][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:57.080][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.081][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.081][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.081][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:57.081][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:57.082][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.082][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.082][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:57.082][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:57.083][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.083][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:57.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:57.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.085][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:57.085][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:57.085][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.085][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.086][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:57.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:57.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.087][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:57.087][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:57.087][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.087][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:57.102][self$createEntryFromContent] Accession numbers: 75174. biodb.TRACE[2025-03-19 18:26:57.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:57.107][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:57.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:57.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:57.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:57.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:57.110][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:57.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:57.111][private$loadEntries] Creating entries from ids [1]: "15441". biodb.DEBUG[2025-03-19 18:26:57.111][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:57.111][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441". biodb.TRACE[2025-03-19 18:26:57.112][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:57.112][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:57.112][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:57.113][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:57.113][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:57.113][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:57.114][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:57.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:57.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:57.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:57.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:57.117][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:57.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:57.117][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441". biodb.DEBUG[2025-03-19 18:26:57.118][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:57.118][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:57.119][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441". biodb.TRACE[2025-03-19 18:26:57.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441). biodb.DEBUG[2025-03-19 18:26:57.872][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:57.873][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content" biodb.TRACE[2025-03-19 18:26:57.874][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request" biodb.TRACE[2025-03-19 18:26:57.878][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml" biodb.DEBUG[2025-03-19 18:26:57.879][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:57.879][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:57.880][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:57.880][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:57.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:57.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:57.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:57.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:57.883][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:57.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:57.884][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.884][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.885][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.885][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.886][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:57.887][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:57.887][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.887][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.887][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:57.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:57.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.888][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:57.889][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:57.889][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.889][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:57.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:57.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.891][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:57.891][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:57.892][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.892][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:57.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.893][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:57.894][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:57.894][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.894][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:57.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:57.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.895][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:57.896][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:57.896][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.896][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.897][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:57.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:57.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.898][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:57.898][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.898][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.898][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.899][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:57.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.900][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:57.900][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:57.900][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.901][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:57.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:57.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.902][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:57.902][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:57.902][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.903][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:57.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:57.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.904][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:57.904][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:57.905][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.905][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.905][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:57.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:57.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.912][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:57.912][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:57.912][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.913][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.913][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:57.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:57.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:57.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:57.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:57.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:57.925][self$createEntryFromContent] Accession numbers: 15441. biodb.TRACE[2025-03-19 18:26:57.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:57.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:57.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:57.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:57.929][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:57.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:57.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:57.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:57.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:57.932][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:57.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:57.932][private$loadEntries] Creating entries from ids [1]: "15442". biodb.DEBUG[2025-03-19 18:26:57.933][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:57.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442". biodb.TRACE[2025-03-19 18:26:57.934][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:57.934][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:57.934][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:57.935][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:57.935][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:57.935][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:57.936][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:57.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:57.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:57.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:57.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:57.939][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:57.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:57.942][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442". biodb.DEBUG[2025-03-19 18:26:57.943][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:57.944][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:57.944][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442". biodb.TRACE[2025-03-19 18:26:58.376][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442). biodb.DEBUG[2025-03-19 18:26:58.736][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:58.737][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content" biodb.TRACE[2025-03-19 18:26:58.738][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request" biodb.TRACE[2025-03-19 18:26:58.739][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml" biodb.DEBUG[2025-03-19 18:26:58.739][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:58.740][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:58.740][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:58.740][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:58.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:58.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:58.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:58.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:58.743][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:58.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:58.744][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.745][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.745][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.745][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.746][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:58.747][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:58.747][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.747][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.748][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:58.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:58.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.749][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:58.749][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:58.749][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.749][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.750][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:58.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.751][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:58.751][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:58.751][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.751][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:58.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:58.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.753][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:58.753][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:58.753][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.754][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:58.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.755][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:58.755][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:58.755][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.756][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.756][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:58.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:58.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.757][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:58.757][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.757][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.758][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.758][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:58.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.759][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:58.759][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:58.759][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.760][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:58.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:58.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.766][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:58.766][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:58.767][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.767][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:58.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:58.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.768][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:58.769][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:58.769][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.769][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.770][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:58.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:58.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.771][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:58.771][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:58.771][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.772][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:58.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:58.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:58.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:58.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:58.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:58.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:58.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:58.783][self$createEntryFromContent] Accession numbers: 15442. biodb.TRACE[2025-03-19 18:26:58.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:58.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:58.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:58.787][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:58.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:58.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:58.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:58.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:58.790][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:58.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:58.791][private$loadEntries] Creating entries from ids [1]: "57310". biodb.DEBUG[2025-03-19 18:26:58.791][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:58.791][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310". biodb.TRACE[2025-03-19 18:26:58.792][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:58.792][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:58.795][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:58.796][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:58.796][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:58.796][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:58.797][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:58.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:58.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:58.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:58.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:58.800][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:58.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:58.801][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310". biodb.DEBUG[2025-03-19 18:26:58.802][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:58.802][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:58.803][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310". biodb.TRACE[2025-03-19 18:26:59.170][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310). biodb.DEBUG[2025-03-19 18:26:59.536][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:26:59.537][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content" biodb.TRACE[2025-03-19 18:26:59.538][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request" biodb.TRACE[2025-03-19 18:26:59.539][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml" biodb.DEBUG[2025-03-19 18:26:59.540][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:26:59.540][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:26:59.541][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:26:59.541][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:59.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:59.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:59.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:59.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:59.544][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:59.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:26:59.545][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.545][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.545][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.546][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.547][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:59.548][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:59.548][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.548][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.548][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:26:59.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:26:59.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.549][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:59.550][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:59.550][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.550][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:26:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:26:59.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.552][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:59.552][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:59.552][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.553][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:26:59.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:26:59.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.554][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:59.554][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:59.555][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.555][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:26:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:26:59.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.556][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:59.557][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:26:59.557][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.557][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.557][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:59.558][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.558][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.562][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.562][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:26:59.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.564][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:59.564][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:59.564][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.564][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:59.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:26:59.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.566][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:59.566][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:59.566][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.567][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:26:59.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:26:59.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.568][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:59.568][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:59.569][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.569][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:26:59.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:26:59.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.570][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:59.570][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:59.571][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.571][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:26:59.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:26:59.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:59.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:59.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:26:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:26:59.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:26:59.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:26:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:59.584][self$createEntryFromContent] Accession numbers: 57310. biodb.TRACE[2025-03-19 18:26:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:26:59.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:26:59.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:26:59.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:26:59.588][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:59.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:59.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:59.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:59.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:59.595][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:59.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:59.596][private$loadEntries] Creating entries from ids [1]: "66216". biodb.DEBUG[2025-03-19 18:26:59.596][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:26:59.597][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216". biodb.TRACE[2025-03-19 18:26:59.597][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:26:59.598][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:26:59.598][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:26:59.598][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:26:59.598][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:26:59.599][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:26:59.600][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:26:59.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:26:59.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:26:59.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:26:59.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:26:59.603][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:26:59.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:26:59.603][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216". biodb.DEBUG[2025-03-19 18:26:59.604][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:26:59.605][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:26:59.605][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216". biodb.TRACE[2025-03-19 18:26:59.967][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216). biodb.DEBUG[2025-03-19 18:27:00.341][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:00.342][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content" biodb.TRACE[2025-03-19 18:27:00.343][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request" biodb.TRACE[2025-03-19 18:27:00.344][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml" biodb.DEBUG[2025-03-19 18:27:00.345][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:00.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:00.346][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:00.346][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:00.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:00.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:00.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:00.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:00.350][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:00.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:00.351][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.352][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.352][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.352][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.354][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:00.354][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:00.354][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.354][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.355][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:00.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:00.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.356][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:00.356][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:00.356][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.356][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:00.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:00.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.358][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:00.358][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:00.358][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.359][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:00.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:00.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.360][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:00.360][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:00.360][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.364][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:00.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:00.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.366][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:00.366][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:00.366][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.366][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.367][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:00.367][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.367][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.368][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.368][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:00.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.369][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:00.369][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:00.369][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.370][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:00.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:00.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.371][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:00.371][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:00.372][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.372][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:00.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.373][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:00.374][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:00.374][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.374][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.374][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:00.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:00.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.375][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:00.376][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:00.376][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.376][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:00.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:00.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:00.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:00.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:00.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:00.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:00.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:00.388][self$createEntryFromContent] Accession numbers: 66216. biodb.TRACE[2025-03-19 18:27:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:00.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:00.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:00.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:00.395][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:00.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:00.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:00.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:00.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:00.398][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:00.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:00.399][private$loadEntries] Creating entries from ids [1]: "70860". biodb.DEBUG[2025-03-19 18:27:00.399][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:00.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860". biodb.TRACE[2025-03-19 18:27:00.400][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:00.400][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:00.401][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:00.401][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:00.401][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:00.401][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:00.402][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:00.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:00.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:00.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:00.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:00.405][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:00.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:00.406][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860". biodb.DEBUG[2025-03-19 18:27:00.406][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:00.407][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:00.407][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860". biodb.TRACE[2025-03-19 18:27:00.768][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860). biodb.DEBUG[2025-03-19 18:27:01.133][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:01.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content" biodb.TRACE[2025-03-19 18:27:01.135][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request" biodb.TRACE[2025-03-19 18:27:01.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml" biodb.DEBUG[2025-03-19 18:27:01.136][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:01.137][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:01.137][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:01.138][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:01.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:01.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:01.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:01.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:01.141][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:01.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:01.142][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.142][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.142][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.142][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.144][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:01.144][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:01.144][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.145][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.145][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:01.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.146][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:01.146][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:01.147][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.147][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:01.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:01.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.152][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:01.152][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:01.152][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.153][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.153][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:01.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:01.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.154][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:01.154][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:01.155][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.155][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:01.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:01.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.156][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:01.156][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:01.157][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.157][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.157][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:01.158][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.158][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.158][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:01.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.159][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.160][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.160][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.160][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.162][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:01.162][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:01.162][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.162][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:01.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:01.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.164][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:01.164][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:01.164][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.164][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:01.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:01.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.166][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:01.166][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:01.166][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.167][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:01.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:01.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:01.180][self$createEntryFromContent] Accession numbers: 70860. biodb.TRACE[2025-03-19 18:27:01.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:01.184][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:01.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:01.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:01.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:01.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:01.187][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:01.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:01.187][private$loadEntries] Creating entries from ids [1]: "70861". biodb.DEBUG[2025-03-19 18:27:01.187][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:01.188][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861". biodb.TRACE[2025-03-19 18:27:01.188][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:01.189][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:01.189][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:01.189][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:01.189][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:01.190][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:01.190][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:01.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:01.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:01.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:01.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:01.193][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:01.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:01.194][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861". biodb.DEBUG[2025-03-19 18:27:01.194][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:01.195][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:01.195][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861". biodb.TRACE[2025-03-19 18:27:01.565][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861). biodb.DEBUG[2025-03-19 18:27:01.946][scheduler$sendRequest] Saving content of request to cache. biodb.INFO [2025-03-19 18:27:01.947][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649". biodb.TRACE[2025-03-19 18:27:01.947][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content" biodb.TRACE[2025-03-19 18:27:01.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request" biodb.TRACE[2025-03-19 18:27:01.949][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml" biodb.DEBUG[2025-03-19 18:27:01.950][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:01.950][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:01.950][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:01.951][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:01.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:01.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:01.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:01.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:01.954][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:01.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:01.955][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.955][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.956][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.956][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.957][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:01.962][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:01.962][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.963][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.963][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:01.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:01.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.964][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:01.964][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:01.964][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.965][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.965][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:01.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:01.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.966][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:01.966][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:01.967][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.967][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:01.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.968][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:01.968][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:01.969][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.969][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:01.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:01.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.970][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:01.970][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:01.971][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.971][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.971][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:01.972][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.972][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.972][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.972][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:01.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.973][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.974][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.974][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.974][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:01.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.975][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:01.976][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:01.976][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.976][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:01.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:01.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.977][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:01.978][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:01.978][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.978][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:01.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:01.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.979][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:01.980][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:01.980][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.980][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:01.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:01.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:01.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:01.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:01.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:01.995][self$createEntryFromContent] Accession numbers: 70861. biodb.TRACE[2025-03-19 18:27:01.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:01.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:01.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:01.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:01.998][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:01.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:01.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:02.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:02.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:02.001][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:02.001][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.DEBUG[2025-03-19 18:27:02.002][private$loadEntries] Creating entries from ids [1]: "78662". biodb.DEBUG[2025-03-19 18:27:02.002][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:02.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662". biodb.TRACE[2025-03-19 18:27:02.003][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:02.003][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:02.004][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:02.004][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:02.004][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:02.004][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:02.005][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:02.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:02.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:02.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:02.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:02.008][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:02.009][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[2025-03-19 18:27:02.009][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662". biodb.DEBUG[2025-03-19 18:27:02.010][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:02.010][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:02.011][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662". biodb.TRACE[2025-03-19 18:27:02.376][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662). biodb.DEBUG[2025-03-19 18:27:02.744][scheduler$sendRequest] Saving content of request to cache. biodb.INFO [2025-03-19 18:27:02.745][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649". biodb.TRACE[2025-03-19 18:27:02.746][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content" biodb.TRACE[2025-03-19 18:27:02.747][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request" biodb.TRACE[2025-03-19 18:27:02.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml" biodb.DEBUG[2025-03-19 18:27:02.748][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:02.748][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:02.749][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:02.749][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:02.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:02.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:02.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:02.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:02.756][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:02.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:02.757][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.757][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.757][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.757][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.759][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:02.759][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:02.759][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.760][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.760][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:02.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:02.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.761][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:02.761][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:02.762][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.762][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:02.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:02.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.763][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:02.763][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:02.764][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.764][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:02.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:02.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.765][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:02.765][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:02.766][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.766][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:02.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:02.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.767][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:02.768][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:02.768][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.768][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.768][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:02.769][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.769][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.769][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.769][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:02.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.770][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:02.771][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:02.771][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.771][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:02.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:02.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.773][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:02.773][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:02.773][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.773][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:02.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:02.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.775][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:02.775][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:02.775][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.775][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.776][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:02.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:02.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.777][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:02.777][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:02.777][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.778][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:02.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:02.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:02.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:02.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:02.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:02.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:02.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:02.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:02.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:02.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:02.793][self$createEntryFromContent] Accession numbers: 78662. biodb.TRACE[2025-03-19 18:27:02.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:02.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:02.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:02.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:02.796][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:02.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:02.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:02.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:02.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:02.798][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:02.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:02.799][private$loadEntries] Creating entries from ids [1]: "85084". biodb.DEBUG[2025-03-19 18:27:02.799][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:02.799][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084". biodb.TRACE[2025-03-19 18:27:02.800][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:02.800][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:02.800][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:02.801][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:02.801][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:02.801][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:02.802][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:02.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:02.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:02.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:02.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:02.804][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:02.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:02.805][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084". biodb.DEBUG[2025-03-19 18:27:02.806][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:02.806][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:02.806][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084". biodb.TRACE[2025-03-19 18:27:03.173][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084). biodb.DEBUG[2025-03-19 18:27:03.528][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:03.529][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content" biodb.TRACE[2025-03-19 18:27:03.533][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request" biodb.TRACE[2025-03-19 18:27:03.536][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml" biodb.DEBUG[2025-03-19 18:27:03.537][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:03.537][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:03.538][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:03.538][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:03.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:03.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:03.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:03.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:03.541][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:03.541][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.TRACE[2025-03-19 18:27:03.542][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.542][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.543][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.543][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.544][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:03.545][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:03.545][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.545][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.545][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:03.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:03.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.546][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:03.547][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:03.547][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.547][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:03.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:03.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.548][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:03.549][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:03.549][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.549][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.549][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:03.550][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:03.550][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.550][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.550][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:03.551][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:03.551][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.551][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.551][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:03.552][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.552][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.552][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.553][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:03.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.554][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:03.554][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:03.554][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.554][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:03.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:03.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.555][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:03.556][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:03.556][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.556][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:03.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:03.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.557][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:03.558][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:03.558][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.558][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.558][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:03.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.559][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:03.560][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:03.560][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.560][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:03.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:03.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:03.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:03.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:03.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:03.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:03.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:03.573][self$createEntryFromContent] Accession numbers: 85084. biodb.TRACE[2025-03-19 18:27:03.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:03.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:03.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:03.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:03.576][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:03.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:03.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:03.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:03.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:03.579][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:03.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:03.579][private$loadEntries] Creating entries from ids [1]: "85086". biodb.DEBUG[2025-03-19 18:27:03.579][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:03.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086". biodb.TRACE[2025-03-19 18:27:03.580][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:03.580][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:03.581][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:03.581][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:03.581][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:03.581][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:03.582][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:03.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:03.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:03.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:03.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:03.585][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:03.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:03.585][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086". biodb.DEBUG[2025-03-19 18:27:03.586][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:03.586][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:03.587][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086". biodb.TRACE[2025-03-19 18:27:04.234][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086). biodb.DEBUG[2025-03-19 18:27:04.599][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:04.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content" biodb.TRACE[2025-03-19 18:27:04.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request" biodb.TRACE[2025-03-19 18:27:04.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml" biodb.DEBUG[2025-03-19 18:27:04.606][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:04.606][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:04.607][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:04.607][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:04.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:04.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:04.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:04.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:04.610][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:04.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:04.611][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.612][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.612][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.612][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.613][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:04.614][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:04.614][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.614][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:04.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.615][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:04.616][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:04.616][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.616][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:04.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.617][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:04.618][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:04.618][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.618][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.618][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:04.619][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:04.619][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.619][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.619][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:04.620][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:04.620][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.620][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.620][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:04.621][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.621][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.621][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.621][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.622][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:04.623][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:04.623][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.623][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:04.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:04.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.624][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:04.624][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:04.625][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.625][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:04.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:04.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.626][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:04.626][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:04.627][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.627][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.627][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.628][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:04.628][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:04.629][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.629][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:04.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:04.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:04.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:04.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:04.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:04.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:04.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:04.641][self$createEntryFromContent] Accession numbers: 85086. biodb.TRACE[2025-03-19 18:27:04.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:04.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:04.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:04.644][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:04.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:04.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:04.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:04.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:04.646][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:04.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:04.647][private$loadEntries] Creating entries from ids [1]: "88123". biodb.DEBUG[2025-03-19 18:27:04.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:04.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123". biodb.TRACE[2025-03-19 18:27:04.648][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:04.648][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:04.648][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:04.649][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:04.649][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:04.649][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:04.650][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:04.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:04.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:04.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:04.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:04.652][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:04.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:04.653][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123". biodb.DEBUG[2025-03-19 18:27:04.654][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:04.654][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:04.654][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123". biodb.TRACE[2025-03-19 18:27:05.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123). biodb.DEBUG[2025-03-19 18:27:05.379][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:05.380][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content" biodb.TRACE[2025-03-19 18:27:05.382][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request" biodb.TRACE[2025-03-19 18:27:05.387][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml" biodb.DEBUG[2025-03-19 18:27:05.388][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:05.389][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:05.389][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:05.390][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:05.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:05.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:05.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:05.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:05.393][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:05.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:05.394][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.394][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.395][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.395][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.397][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:05.397][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:05.397][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.397][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.398][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:05.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:05.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.399][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:05.399][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:05.399][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.400][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:05.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:05.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.401][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:05.401][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:05.402][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.402][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:05.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:05.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.403][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:05.403][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:05.404][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.404][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:05.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:05.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.405][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:05.406][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:05.406][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.406][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.406][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:05.407][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.407][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.407][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.408][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:05.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.409][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:05.409][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:05.409][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.410][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:05.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:05.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.411][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:05.411][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:05.412][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.412][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:05.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:05.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.413][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:05.414][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:05.414][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.414][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.414][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:05.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:05.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.415][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:05.418][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:05.419][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.419][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:05.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:05.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:05.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:05.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:05.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:05.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:05.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:05.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:05.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:05.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:05.432][self$createEntryFromContent] Accession numbers: 88123. biodb.TRACE[2025-03-19 18:27:05.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:05.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:05.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:05.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:05.436][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:05.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:05.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:05.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:05.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:05.439][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:05.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:05.439][private$loadEntries] Creating entries from ids [1]: "134117". biodb.DEBUG[2025-03-19 18:27:05.440][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:05.440][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117". biodb.TRACE[2025-03-19 18:27:05.441][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:05.441][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:05.441][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:05.442][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:05.442][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:05.442][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:05.443][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:05.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:05.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:05.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:05.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:05.446][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:05.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:05.446][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117". biodb.DEBUG[2025-03-19 18:27:05.447][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:05.450][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:05.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117". biodb.TRACE[2025-03-19 18:27:05.855][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117). biodb.DEBUG[2025-03-19 18:27:06.219][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:06.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content" biodb.TRACE[2025-03-19 18:27:06.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request" biodb.TRACE[2025-03-19 18:27:06.222][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml" biodb.DEBUG[2025-03-19 18:27:06.223][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:06.223][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:06.223][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:06.224][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:06.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:06.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:06.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:06.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:06.227][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:06.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:06.228][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.228][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.228][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.228][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.230][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:06.230][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:06.230][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.231][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.231][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:06.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:06.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.232][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:06.232][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:06.232][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.233][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:06.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:06.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.234][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:06.234][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:06.235][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.235][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:06.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:06.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.236][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:06.236][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:06.237][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.237][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:06.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:06.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.238][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:06.239][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:06.239][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.239][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.239][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:06.240][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.240][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.240][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.240][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:06.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.241][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:06.242][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:06.242][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.242][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:06.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:06.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.243][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:06.244][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:06.244][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.244][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:06.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.249][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:06.249][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:06.250][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.250][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.250][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:06.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:06.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.251][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:06.252][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:06.252][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.252][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.252][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:06.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:06.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:06.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:06.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:06.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:06.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:06.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:06.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:06.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:06.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:06.264][self$createEntryFromContent] Accession numbers: 134117. biodb.TRACE[2025-03-19 18:27:06.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:06.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:06.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:06.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:06.267][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:06.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:06.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:06.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:06.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:06.270][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:06.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:06.270][private$loadEntries] Creating entries from ids [1]: "138307". biodb.DEBUG[2025-03-19 18:27:06.271][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:06.271][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307". biodb.TRACE[2025-03-19 18:27:06.272][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:06.272][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:06.272][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:06.272][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:06.273][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:06.273][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:06.274][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:06.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:06.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:06.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:06.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:06.279][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:06.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:06.280][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307". biodb.DEBUG[2025-03-19 18:27:06.281][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:06.281][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:06.281][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307". biodb.TRACE[2025-03-19 18:27:06.655][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307). biodb.DEBUG[2025-03-19 18:27:07.008][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:07.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content" biodb.TRACE[2025-03-19 18:27:07.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request" biodb.TRACE[2025-03-19 18:27:07.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml" biodb.DEBUG[2025-03-19 18:27:07.011][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:07.012][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:07.012][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:07.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:07.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:07.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:07.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:07.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:07.015][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:07.015][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.TRACE[2025-03-19 18:27:07.016][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.016][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.016][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.017][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.018][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:07.018][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:07.018][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.019][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.019][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:07.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:07.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.020][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:07.020][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:07.020][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.021][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.021][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:07.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:07.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.022][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:07.022][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:07.022][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.023][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:07.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:07.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.024][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:07.024][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:07.024][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.025][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:07.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:07.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.026][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:07.026][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:07.026][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.026][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.027][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:07.027][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.027][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.027][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.028][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:07.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.029][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.032][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.033][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.033][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.035][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:07.035][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:07.035][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.036][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:07.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:07.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.037][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:07.037][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:07.037][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.038][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.038][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:07.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:07.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.039][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:07.039][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:07.039][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.040][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.040][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:07.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:07.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:07.050][self$createEntryFromContent] Accession numbers: 138307. biodb.TRACE[2025-03-19 18:27:07.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:07.053][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:07.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:07.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:07.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:07.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:07.056][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:07.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:07.059][private$loadEntries] Creating entries from ids [1]: "176803". biodb.DEBUG[2025-03-19 18:27:07.059][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:07.060][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803". biodb.TRACE[2025-03-19 18:27:07.060][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:07.061][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:07.061][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:07.061][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:07.061][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:07.062][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:07.062][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:07.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:07.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:07.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:07.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:07.065][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:07.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:07.065][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803". biodb.DEBUG[2025-03-19 18:27:07.066][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:07.066][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:07.067][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803". biodb.TRACE[2025-03-19 18:27:07.437][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803). biodb.DEBUG[2025-03-19 18:27:07.796][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:07.796][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content" biodb.TRACE[2025-03-19 18:27:07.798][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request" biodb.TRACE[2025-03-19 18:27:07.799][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml" biodb.DEBUG[2025-03-19 18:27:07.799][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:07.799][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:07.800][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:07.800][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:07.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:07.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:07.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:07.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:07.803][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:07.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:07.804][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.805][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.805][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.805][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.807][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:07.807][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:07.807][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.808][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:07.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:07.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.809][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:07.809][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:07.809][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.810][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:07.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:07.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.811][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:07.811][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:07.812][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.812][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:07.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:07.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.813][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:07.813][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:07.814][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.814][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:07.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:07.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.819][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:07.820][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:07.820][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.821][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.821][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:07.821][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.822][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.822][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.822][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:07.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.823][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.823][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.824][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.824][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:07.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.825][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:07.826][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:07.826][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.826][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:07.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:07.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.828][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:07.828][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:07.828][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.828][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.829][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:07.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:07.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.830][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:07.830][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:07.830][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.830][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.831][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:07.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:07.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:07.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:07.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:07.842][self$createEntryFromContent] Accession numbers: 176803. biodb.TRACE[2025-03-19 18:27:07.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:07.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:07.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:07.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:07.848][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:07.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:07.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:07.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:07.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:07.851][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:07.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:07.851][private$loadEntries] Creating entries from ids [1]: "176962". biodb.DEBUG[2025-03-19 18:27:07.852][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:07.852][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962". biodb.TRACE[2025-03-19 18:27:07.852][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:07.853][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:07.853][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:07.853][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:07.854][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:07.854][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:07.855][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:07.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:07.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:07.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:07.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:07.857][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:07.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:07.858][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962". biodb.DEBUG[2025-03-19 18:27:07.858][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:07.859][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:07.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962". biodb.TRACE[2025-03-19 18:27:08.221][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962). biodb.DEBUG[2025-03-19 18:27:08.587][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:08.588][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content" biodb.TRACE[2025-03-19 18:27:08.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request" biodb.TRACE[2025-03-19 18:27:08.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml" biodb.DEBUG[2025-03-19 18:27:08.590][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:08.590][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:08.591][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:08.591][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:08.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:08.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:08.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:08.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:08.594][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:08.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:08.595][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.595][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.595][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.595][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.597][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:08.597][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:08.597][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.597][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:08.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:08.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.599][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:08.599][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:08.599][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.599][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:08.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.600][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:08.601][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:08.603][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.604][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:08.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:08.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.606][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:08.606][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:08.606][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.606][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:08.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:08.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.607][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:08.608][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:08.608][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.608][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.608][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:08.609][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.609][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.609][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:08.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.610][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:08.611][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:08.611][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.611][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:08.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:08.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.612][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:08.612][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:08.613][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.613][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:08.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:08.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.614][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:08.614][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:08.615][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.615][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:08.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:08.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.616][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:08.616][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:08.616][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.617][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.617][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:08.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:08.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:08.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:08.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:08.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:08.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:08.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:08.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:08.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:08.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:08.629][self$createEntryFromContent] Accession numbers: 176962. biodb.TRACE[2025-03-19 18:27:08.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:08.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:08.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:08.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:08.632][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:08.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:08.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:08.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:08.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:08.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:08.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:08.635][private$loadEntries] Creating entries from ids [1]: "198655". biodb.DEBUG[2025-03-19 18:27:08.635][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:08.635][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655". biodb.TRACE[2025-03-19 18:27:08.635][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:08.636][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:08.636][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:08.636][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:08.636][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:08.637][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:08.637][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:08.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:08.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:08.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:08.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:08.640][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:08.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:08.640][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655". biodb.DEBUG[2025-03-19 18:27:08.641][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:08.641][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:08.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655". biodb.TRACE[2025-03-19 18:27:09.001][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655). biodb.DEBUG[2025-03-19 18:27:09.920][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:09.920][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content" biodb.TRACE[2025-03-19 18:27:09.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request" biodb.TRACE[2025-03-19 18:27:09.923][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml" biodb.DEBUG[2025-03-19 18:27:09.923][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:09.923][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:09.924][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:09.924][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:09.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:09.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:09.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:09.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:09.927][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:09.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:09.928][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.928][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.929][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.929][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.930][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:09.931][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:09.931][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.931][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.935][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:09.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:09.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.937][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:09.937][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:09.937][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.937][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:09.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:09.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.939][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:09.939][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:09.939][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.940][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:09.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:09.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.941][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:09.941][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:09.942][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.942][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:09.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:09.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.943][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:09.943][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:09.944][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.944][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.944][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:09.945][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.945][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.945][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.945][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:09.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.946][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:09.947][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:09.947][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.947][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:09.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:09.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.948][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:09.949][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:09.949][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.949][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:09.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:09.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.951][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:09.951][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:09.951][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.951][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.952][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:09.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:09.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.953][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:09.953][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:09.953][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.953][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.954][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:09.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:09.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:09.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:09.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:09.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:09.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:09.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:09.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:09.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:09.968][self$createEntryFromContent] Accession numbers: 198655. biodb.TRACE[2025-03-19 18:27:09.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:09.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:09.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:09.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:09.971][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:09.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:09.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:09.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:09.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:09.974][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:09.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:09.975][private$loadEntries] Creating entries from ids [1]: "215045". biodb.DEBUG[2025-03-19 18:27:09.975][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:09.975][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045". biodb.TRACE[2025-03-19 18:27:09.976][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:09.976][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:09.976][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:09.976][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:09.977][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:09.977][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:09.978][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:09.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:09.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:09.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:09.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:09.980][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:09.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:09.981][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045". biodb.DEBUG[2025-03-19 18:27:09.982][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:09.982][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:09.983][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045". biodb.TRACE[2025-03-19 18:27:10.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045). biodb.DEBUG[2025-03-19 18:27:10.729][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:10.730][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content" biodb.TRACE[2025-03-19 18:27:10.732][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request" biodb.TRACE[2025-03-19 18:27:10.732][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml" biodb.DEBUG[2025-03-19 18:27:10.733][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:10.733][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:10.734][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:10.734][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:10.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:10.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:10.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:10.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:10.741][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:10.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:10.743][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.743][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.743][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.743][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.745][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:10.745][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:10.745][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.746][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.746][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:10.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:10.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.747][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:10.747][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:10.748][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.748][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.748][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:10.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:10.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.750][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:10.750][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:10.750][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.750][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:10.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:10.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.752][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:10.752][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:10.752][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.753][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:10.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.754][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:10.754][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:10.754][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.755][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.755][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:10.755][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.756][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.756][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.756][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:10.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.757][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:10.758][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:10.758][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.758][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:10.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:10.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.760][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:10.760][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:10.760][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.760][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:10.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:10.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.762][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:10.762][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:10.762][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.763][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.763][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:10.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:10.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.764][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:10.764][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:10.765][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.765][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.765][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:10.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:10.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:10.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:10.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:10.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:10.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:10.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:10.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:10.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:10.781][self$createEntryFromContent] Accession numbers: 215045. biodb.TRACE[2025-03-19 18:27:10.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:10.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:10.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:10.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:10.790][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:10.792][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:10.792][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:10.793][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:11.305][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:11.810][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:11.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content" biodb.TRACE[2025-03-19 18:27:11.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request" biodb.DEBUG[2025-03-19 18:27:11.814][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.817][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.825][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.828][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.834][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.837][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.843][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.846][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.932][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.935][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.939][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.941][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.941][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.TRACE[2025-03-19 18:27:11.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.945][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.947][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.951][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.953][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.957][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.959][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.963][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.966][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.970][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.973][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.977][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.980][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.984][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.987][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.991][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:11.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:11.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:11.994][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:11.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:11.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:11.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:11.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:11.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:11.998][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:11.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:11.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:12.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:12.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:12.001][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:12.001][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[2025-03-19 18:27:12.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:12.005][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:12.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:12.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:12.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:12.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:12.008][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:12.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:12.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:12.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:12.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:12.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:12.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:12.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:12.015][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:12.015][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.TRACE[2025-03-19 18:27:12.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:12.019][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:12.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:12.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:12.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:12.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:12.022][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:12.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:12.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:12.026][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:12.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:12.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:12.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:12.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:12.029][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:12.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:12.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:12.033][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:12.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:12.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:12.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:12.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:12.036][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:12.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:12.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:12.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:12.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:12.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:12.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:12.060][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:12.061][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:12.061][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:12.062][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:12.422][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:12.910][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:12.910][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content" biodb.TRACE[2025-03-19 18:27:12.912][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request" biodb.DEBUG[2025-03-19 18:27:12.913][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:12.914][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:12.914][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:12.915][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:13.264][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:13.618][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:13.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content" biodb.TRACE[2025-03-19 18:27:13.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request" biodb.DEBUG[2025-03-19 18:27:13.621][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:13.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:13.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:13.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:13.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:13.624][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:13.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:13.625][private$loadEntries] Creating entries from ids [1]: "4648". biodb.DEBUG[2025-03-19 18:27:13.625][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:13.626][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648". biodb.TRACE[2025-03-19 18:27:13.626][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:13.626][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:13.627][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:13.627][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:13.627][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:13.628][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:13.629][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:13.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:13.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:13.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:13.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:13.631][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:13.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:13.632][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648". biodb.DEBUG[2025-03-19 18:27:13.633][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:13.633][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:13.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648". biodb.TRACE[2025-03-19 18:27:13.995][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648). biodb.DEBUG[2025-03-19 18:27:14.365][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:14.366][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content" biodb.TRACE[2025-03-19 18:27:14.367][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request" biodb.TRACE[2025-03-19 18:27:14.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml" biodb.DEBUG[2025-03-19 18:27:14.369][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:14.369][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:14.369][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:14.370][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:14.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:14.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:14.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:14.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:14.373][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:14.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:14.374][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.374][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.374][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.374][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.376][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:14.376][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:14.376][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.377][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.377][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:14.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.378][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:14.378][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:14.378][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.379][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:14.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:14.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.380][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:14.380][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:14.380][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.381][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:14.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:14.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.382][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:14.382][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:14.382][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.383][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:14.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:14.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.384][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:14.384][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:14.384][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.384][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.385][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:14.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:14.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.386][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:14.386][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:14.386][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.386][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.387][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:14.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:14.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.388][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.388][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.388][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.389][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.390][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:14.390][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:14.390][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.391][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:14.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:14.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.392][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:14.392][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:14.393][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.393][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.393][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:14.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.394][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:14.395][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:14.395][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.395][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.395][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:14.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:14.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:14.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:14.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:14.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:14.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:14.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:14.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:14.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:14.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:14.406][self$createEntryFromContent] Accession numbers: 4648. biodb.TRACE[2025-03-19 18:27:14.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:14.409][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:14.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:14.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:14.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:14.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:14.412][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:14.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:14.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:14.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:14.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:14.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:14.415][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:14.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:14.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:14.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:14.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:14.418][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:14.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:14.418][private$loadEntries] Creating entries from ids [1]: "62447". biodb.DEBUG[2025-03-19 18:27:14.419][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:14.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447". biodb.TRACE[2025-03-19 18:27:14.424][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:14.425][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:14.425][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:14.425][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:14.425][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:14.426][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:14.427][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:14.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:14.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:14.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:14.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:14.429][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:14.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:14.430][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447". biodb.DEBUG[2025-03-19 18:27:14.431][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:14.431][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:14.432][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447". biodb.TRACE[2025-03-19 18:27:14.791][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447). biodb.DEBUG[2025-03-19 18:27:15.151][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:15.152][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content" biodb.TRACE[2025-03-19 18:27:15.153][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request" biodb.TRACE[2025-03-19 18:27:15.154][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml" biodb.DEBUG[2025-03-19 18:27:15.155][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:15.155][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:15.155][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:15.156][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.159][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.160][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.160][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.160][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.160][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.162][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:15.162][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:15.162][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.163][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.163][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:15.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:15.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.164][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:15.164][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:15.165][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.165][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:15.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:15.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.166][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:15.166][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:15.167][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.167][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:15.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:15.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.168][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:15.168][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:15.169][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.169][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:15.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:15.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.170][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:15.170][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:15.171][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.171][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.171][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:15.172][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.172][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.172][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.172][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:15.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.173][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.174][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.174][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.174][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.176][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:15.176][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:15.176][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.176][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:15.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:15.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.178][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:15.178][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:15.178][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.178][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.179][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:15.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:15.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.180][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:15.180][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:15.180][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.181][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:15.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:15.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:15.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:15.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:15.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:15.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:15.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:15.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:15.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.192][self$createEntryFromContent] Accession numbers: 62447. biodb.TRACE[2025-03-19 18:27:15.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.202][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:15.203][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:15.204][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2025-03-19 18:27:15.204][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:15.204][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2025-03-19 18:27:15.205][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.208][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.208][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.TRACE[2025-03-19 18:27:15.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.211][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.214][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.214][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.TRACE[2025-03-19 18:27:15.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.220][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.222][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.223][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". biodb.TRACE[2025-03-19 18:27:15.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.228][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.231][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.236][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.239][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.239][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.TRACE[2025-03-19 18:27:15.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.243][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.249][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.253][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.255][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.256][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.TRACE[2025-03-19 18:27:15.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.259][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.262][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.265][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.268][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.272][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.274][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.278][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.281][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.281][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.TRACE[2025-03-19 18:27:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.284][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.287][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.290][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.293][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.296][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.299][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.302][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.305][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.309][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.311][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.312][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.TRACE[2025-03-19 18:27:15.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.315][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.318][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.321][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.324][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.327][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.330][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.333][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.336][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.336][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[2025-03-19 18:27:15.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.345][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:15.347][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:15.347][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2025-03-19 18:27:15.347][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:15.348][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2025-03-19 18:27:15.351][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.354][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.357][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.360][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.365][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.368][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.368][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[2025-03-19 18:27:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.373][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.376][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.382][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.384][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.388][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.391][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.394][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.397][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.397][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[2025-03-19 18:27:15.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.400][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.403][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.403][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.TRACE[2025-03-19 18:27:15.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.407][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.409][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.413][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.415][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.419][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.422][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.422][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[2025-03-19 18:27:15.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.425][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.428][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.432][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.435][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.438][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.441][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.445][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.447][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.454][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.456][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.460][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.462][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.466][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.468][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.468][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[2025-03-19 18:27:15.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.472][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.474][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.475][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[2025-03-19 18:27:15.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.478][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.480][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:15.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:15.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.488][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-03-19 18:27:15.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-03-19 18:27:15.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-03-19 18:27:15.492][biodb::testThat] biodb.INFO [2025-03-19 18:27:15.492][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2025-03-19 18:27:15.493][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:15.493][biodb::testThat] biodb.TRACE[2025-03-19 18:27:15.494][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-03-19 18:27:15.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-03-19 18:27:15.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:15.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:15.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:15.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:15.500][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:15.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:15.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:15.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:15.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:15.503][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:15.503][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.DEBUG[2025-03-19 18:27:15.504][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:15.505][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:15.506][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:15.506][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:16.164][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:16.824][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:16.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content" biodb.TRACE[2025-03-19 18:27:16.826][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request" biodb.DEBUG[2025-03-19 18:27:16.827][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:16.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:16.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:16.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:16.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:16.832][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:16.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:16.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:16.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:16.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:16.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:16.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:16.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:16.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:16.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:16.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:16.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:16.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:16.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:16.835][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:16.836][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:16.837][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:16.837][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:17.193][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:17.548][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:17.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content" biodb.TRACE[2025-03-19 18:27:17.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request" biodb.DEBUG[2025-03-19 18:27:17.551][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:17.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:17.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:17.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:17.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:17.554][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:17.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:17.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:17.558][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:17.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:17.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:17.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:17.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:17.561][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:17.561][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[2025-03-19 18:27:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:17.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:17.565][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-03-19 18:27:17.565][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:17.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:17.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:17.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:17.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:17.568][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:17.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:17.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.571][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.571][private$selectFields] biodb.TRACE[2025-03-19 18:27:17.572][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:17.572][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:17.572][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.572][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.573][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.573][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.573][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.573][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.574][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.574][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.574][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.574][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.575][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.575][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.575][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.575][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.576][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.576][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:17.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.586][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2025-03-19 18:27:17.587][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:17.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:17.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:17.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:17.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:17.590][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:17.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:17.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.593][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.593][private$selectFields] biodb.TRACE[2025-03-19 18:27:17.593][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:17.593][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:17.594][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.594][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.594][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.595][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.595][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.595][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.595][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.596][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.596][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.596][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.596][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.597][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.597][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.597][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.597][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.598][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:17.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.601][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-03-19 18:27:17.601][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:17.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:17.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:17.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:17.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:17.604][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:17.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:17.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.607][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.607][private$selectFields] biodb.TRACE[2025-03-19 18:27:17.607][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:17.608][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:17.608][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.608][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.608][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.609][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.609][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.609][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.609][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.610][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.610][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.610][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.610][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:17.611][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.611][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.611][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.611][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.612][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:17.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:17.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.615][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2025-03-19 18:27:17.615][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-03-19 18:27:17.616][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-03-19 18:27:17.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:17.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:17.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:17.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:17.640][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:17.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:17.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:17.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:17.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:17.642][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:17.643][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[2025-03-19 18:27:17.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:17.644][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:17.645][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:17.645][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:18.046][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:18.409][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:18.410][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content" biodb.TRACE[2025-03-19 18:27:18.412][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request" biodb.DEBUG[2025-03-19 18:27:18.413][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:18.414][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:18.414][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:18.415][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:18.777][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:19.153][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:19.154][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content" biodb.TRACE[2025-03-19 18:27:19.156][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request" biodb.DEBUG[2025-03-19 18:27:19.157][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.160][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.163][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.166][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.170][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.172][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.183][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-03-19 18:27:19.195][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.198][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.201][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.201][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.201][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.201][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.202][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.202][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.202][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.202][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.203][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.203][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.203][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.203][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.204][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.204][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.204][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.204][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.205][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.205][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.205][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.205][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.209][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2025-03-19 18:27:19.209][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.212][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.224][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.225][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.225][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.225][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.225][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.226][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.226][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.226][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.226][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.227][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.227][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.227][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.227][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.228][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.231][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.231][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.231][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.231][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.232][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.232][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.235][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-03-19 18:27:19.236][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.238][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.241][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.241][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.241][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.241][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.242][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.242][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.242][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.242][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.242][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.243][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.243][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.243][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.243][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.244][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.244][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.244][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.244][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.244][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.245][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.245][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.248][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2025-03-19 18:27:19.248][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-03-19 18:27:19.249][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-03-19 18:27:19.251][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-03-19 18:27:19.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-03-19 18:27:19.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-03-19 18:27:19.253][biodb::testThat] biodb.INFO [2025-03-19 18:27:19.254][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2025-03-19 18:27:19.254][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:19.254][biodb::testThat] biodb.TRACE[2025-03-19 18:27:19.255][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-03-19 18:27:19.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-03-19 18:27:19.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.261][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.263][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:19.264][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.265][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.266][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2025-03-19 18:27:19.266][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.266][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2025-03-19 18:27:19.267][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.269][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.274][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2025-03-19 18:27:19.274][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.275][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2025-03-19 18:27:19.276][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.278][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.284][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.286][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.289][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-03-19 18:27:19.290][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.292][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.292][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[2025-03-19 18:27:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.295][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.295][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.295][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.295][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.295][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.296][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.296][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.296][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.296][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.297][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.297][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.297][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.297][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.298][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.298][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.298][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.298][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.299][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.299][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.299][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.302][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2025-03-19 18:27:19.303][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.305][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.308][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.308][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.308][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.308][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.308][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.309][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.309][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.309][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.309][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.310][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.310][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.310][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.310][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.311][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.311][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.311][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.312][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.312][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.312][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.312][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.316][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-03-19 18:27:19.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.318][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.321][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.321][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.321][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.321][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.322][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.322][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.322][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.322][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.322][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.323][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.323][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.323][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.323][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.324][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.324][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.324][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.324][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.324][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.325][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.325][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.328][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2025-03-19 18:27:19.328][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-03-19 18:27:19.328][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-03-19 18:27:19.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.336][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.338][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:19.339][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.340][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.340][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2025-03-19 18:27:19.340][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.341][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2025-03-19 18:27:19.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.343][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.343][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2025-03-19 18:27:19.343][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.344][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2025-03-19 18:27:19.344][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.347][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.350][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.352][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.356][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.358][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.362][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-03-19 18:27:19.362][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.365][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.367][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.368][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.368][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.368][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.368][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.369][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.369][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.369][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.369][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.370][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.370][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.370][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.370][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.371][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.371][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.371][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.371][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.372][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.372][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.372][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.378][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2025-03-19 18:27:19.378][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.381][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.383][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.384][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.384][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.384][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.384][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.385][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.385][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.385][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.385][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.386][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.386][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.386][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.386][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.386][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.387][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.387][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.387][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.387][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.388][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.388][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.391][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-03-19 18:27:19.391][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.394][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.396][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.397][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.397][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.397][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.397][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.398][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.398][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.398][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.398][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.399][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.399][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.399][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.399][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.400][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.400][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.400][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.400][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.401][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.401][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.401][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.404][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2025-03-19 18:27:19.405][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-03-19 18:27:19.405][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-03-19 18:27:19.408][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-03-19 18:27:19.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-03-19 18:27:19.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-03-19 18:27:19.410][biodb::testThat] biodb.INFO [2025-03-19 18:27:19.410][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2025-03-19 18:27:19.411][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:19.411][biodb::testThat] biodb.TRACE[2025-03-19 18:27:19.412][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2025-03-19 18:27:19.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2025-03-19 18:27:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.418][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.421][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:19.422][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.423][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2025-03-19 18:27:19.424][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.424][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2025-03-19 18:27:19.425][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.428][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.432][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.433][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.433][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2025-03-19 18:27:19.433][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.434][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2025-03-19 18:27:19.434][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.437][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.440][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.443][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:19.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.446][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-03-19 18:27:19.447][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.449][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.451][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.452][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.452][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.452][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.452][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.452][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.453][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.453][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.453][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.453][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.454][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.454][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.454][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.454][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.454][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.455][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.455][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.455][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.455][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.456][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.459][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2025-03-19 18:27:19.459][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.461][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.464][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.464][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.464][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.464][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.465][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.465][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.465][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.465][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.466][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.466][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.466][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.466][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.467][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.467][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.467][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.467][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.467][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.468][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.468][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.468][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.474][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-03-19 18:27:19.474][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.477][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.479][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.479][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.480][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.480][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.480][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.480][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.481][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.481][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.481][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.481][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.482][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.482][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.482][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.482][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.483][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.483][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.483][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.483][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.483][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.484][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.487][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2025-03-19 18:27:19.487][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-03-19 18:27:19.488][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-03-19 18:27:19.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.499][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.501][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:19.503][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.504][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.504][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2025-03-19 18:27:19.504][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.505][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2025-03-19 18:27:19.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:19.507][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:19.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2025-03-19 18:27:19.508][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:19.508][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2025-03-19 18:27:19.509][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.511][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.515][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.517][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.518][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.TRACE[2025-03-19 18:27:19.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.521][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.523][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.523][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.TRACE[2025-03-19 18:27:19.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:19.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:19.527][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2025-03-19 18:27:19.527][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.530][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.533][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.533][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.533][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.533][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.533][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.534][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.534][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.534][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.534][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.535][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.535][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.535][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.535][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.536][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.536][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.536][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.536][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.537][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.537][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.537][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.541][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2025-03-19 18:27:19.541][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.544][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:19.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.546][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.546][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.547][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.547][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.547][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.547][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.548][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.548][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.548][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.548][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.548][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.549][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.549][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.549][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.549][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.550][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.550][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.550][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.550][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.551][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.554][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2025-03-19 18:27:19.554][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.557][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.557][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.TRACE[2025-03-19 18:27:19.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.559][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.559][private$selectFields] biodb.TRACE[2025-03-19 18:27:19.560][private$selectFields] Fields is null: FALSE biodb.TRACE[2025-03-19 18:27:19.560][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2025-03-19 18:27:19.560][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.560][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.561][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.561][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.561][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.561][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.562][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.562][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.562][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.562][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.563][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2025-03-19 18:27:19.563][ef$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.563][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.563][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.564][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.564][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2025-03-19 18:27:19.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:19.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:19.567][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2025-03-19 18:27:19.567][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2025-03-19 18:27:19.568][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2025-03-19 18:27:19.576][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2025-03-19 18:27:19.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2025-03-19 18:27:19.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:19.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2025-03-19 18:27:19.578][biodb::testThat] biodb.INFO [2025-03-19 18:27:19.579][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL "). biodb.INFO [2025-03-19 18:27:19.579][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:19.579][biodb::testThat] biodb.DEBUG[2025-03-19 18:27:19.580][private$loadEntries] Creating entries from ids [1]: "WRONGA". biodb.DEBUG[2025-03-19 18:27:19.580][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:19.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA". biodb.TRACE[2025-03-19 18:27:19.581][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:19.581][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:19.581][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:19.581][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:19.582][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:19.582][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:19.583][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:19.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:19.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:19.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:19.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:19.585][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:19.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:19.586][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA". biodb.DEBUG[2025-03-19 18:27:19.587][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:19.587][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:19.587][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA". biodb.TRACE[2025-03-19 18:27:19.938][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA). biodb.DEBUG[2025-03-19 18:27:20.295][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:20.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content" biodb.TRACE[2025-03-19 18:27:20.297][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request" biodb.TRACE[2025-03-19 18:27:20.298][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml" biodb.DEBUG[2025-03-19 18:27:20.298][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:20.299][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:20.299][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:20.300][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:20.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:20.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:20.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:20.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:20.302][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:20.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:20.303][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.304][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.304][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.304][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.306][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:20.306][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:20.306][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.306][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.307][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:20.307][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:20.307][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.307][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.308][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:20.308][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:20.308][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.309][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.309][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:20.309][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:20.309][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.310][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.310][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:20.310][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:20.310][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.311][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.311][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:20.311][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:20.312][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.312][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.312][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:20.312][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:20.313][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.313][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.313][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:20.313][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:20.314][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.314][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.314][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:20.315][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:20.315][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.315][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.315][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:20.316][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:20.316][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.316][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:20.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:20.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:20.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:20.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:20.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:20.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:20.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:20.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:20.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:20.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:20.327][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2025-03-19 18:27:20.327][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2025-03-19 18:27:20.330][biodb::testThat] biodb.INFO [2025-03-19 18:27:20.330][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones "). biodb.INFO [2025-03-19 18:27:20.330][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:20.331][biodb::testThat] biodb.DEBUG[2025-03-19 18:27:20.335][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799" biodb.DEBUG[2025-03-19 18:27:20.335][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799". biodb.DEBUG[2025-03-19 18:27:20.335][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)... biodb.TRACE[2025-03-19 18:27:20.336][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799". biodb.TRACE[2025-03-19 18:27:20.336][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE". biodb.TRACE[2025-03-19 18:27:20.337][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:20.337][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:20.337][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:20.338][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:20.338][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:20.339][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:20.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:20.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:20.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:20.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:20.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:20.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:20.343][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB". biodb.DEBUG[2025-03-19 18:27:20.344][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:20.344][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:20.345][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB". biodb.TRACE[2025-03-19 18:27:20.698][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB). biodb.DEBUG[2025-03-19 18:27:21.057][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:21.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content" biodb.TRACE[2025-03-19 18:27:21.059][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request" biodb.DEBUG[2025-03-19 18:27:21.060][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:21.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:21.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:21.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:21.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:21.062][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:21.063][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[2025-03-19 18:27:21.063][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". biodb.DEBUG[2025-03-19 18:27:21.064][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:21.064][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:21.064][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". biodb.TRACE[2025-03-19 18:27:21.419][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528). biodb.DEBUG[2025-03-19 18:27:21.779][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:21.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content" biodb.TRACE[2025-03-19 18:27:21.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request" biodb.DEBUG[2025-03-19 18:27:21.781][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:21.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:21.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:21.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:21.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:21.784][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:21.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:21.785][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". biodb.DEBUG[2025-03-19 18:27:21.786][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:21.786][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:21.787][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". biodb.TRACE[2025-03-19 18:27:22.143][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799). biodb.DEBUG[2025-03-19 18:27:22.507][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:22.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content" biodb.TRACE[2025-03-19 18:27:22.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request" biodb.TRACE[2025-03-19 18:27:22.510][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml" biodb.DEBUG[2025-03-19 18:27:22.510][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:22.511][self$createEntryFromContent] Creating ChEBI entries from 3 content(s). biodb.DEBUG[2025-03-19 18:27:22.511][self$createEntryFromContent] Parsing 3 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:22.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:22.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:22.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:22.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:22.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:22.515][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:22.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:22.516][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.516][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.516][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.516][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.518][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:22.518][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:22.518][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.519][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.519][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:22.519][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:22.519][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.520][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.520][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:22.520][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:22.521][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.521][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.521][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:22.521][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:22.522][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.522][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.522][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.522][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.523][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.523][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.523][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:22.524][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:22.524][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.524][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.524][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.525][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.525][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.525][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.525][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:22.526][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:22.526][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.526][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.527][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:22.527][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:22.527][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.527][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.528][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:22.528][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:22.528][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.528][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:22.545][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:22.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:22.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:22.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:22.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:22.549][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:22.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:22.550][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.550][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.550][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.550][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.552][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:22.552][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:22.553][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.553][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.553][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:22.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:22.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.554][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:22.555][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:22.555][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.555][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:22.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:22.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.557][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:22.557][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:22.557][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.558][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:22.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:22.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.559][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:22.559][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:22.559][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.560][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:22.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:22.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.561][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.562][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.562][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.562][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.562][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.563][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:22.564][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:22.564][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.564][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.565][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:22.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:22.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.566][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.566][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.566][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.566][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.568][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:22.568][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:22.568][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.568][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:22.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:22.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.570][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:22.570][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:22.571][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.571][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:22.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:22.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.572][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:22.572][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:22.573][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.573][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.573][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:22.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:22.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:22.582][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:22.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:22.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:22.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:22.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:22.585][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:22.586][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[2025-03-19 18:27:22.587][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.587][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.587][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.588][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.589][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:22.590][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:22.590][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.590][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.590][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:22.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:22.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.592][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:22.592][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:22.592][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.592][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.593][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:22.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:22.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.594][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:22.594][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:22.594][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.595][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:22.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:22.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.596][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:22.596][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:22.597][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.597][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:22.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:22.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.598][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.599][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.599][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.599][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.599][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:22.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.601][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:22.601][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:22.601][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.601][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.602][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:22.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:22.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.603][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.603][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.603][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.604][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:22.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.605][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:22.605][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:22.605][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.606][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:22.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:22.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.607][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:22.607][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:22.608][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.608][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.608][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:22.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:22.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.609][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:22.610][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:22.610][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.610][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:22.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:22.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:22.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:22.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:22.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:22.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:22.628][self$createEntryFromContent] Accession numbers: , 2528, 7799. biodb.DEBUG[2025-03-19 18:27:22.629][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2025-03-19 18:27:22.629][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>" biodb.INFO [2025-03-19 18:27:22.634][biodb::testThat] biodb.INFO [2025-03-19 18:27:22.634][biodb::testThat] Running test function test.peak.table (" The peak table is correct. "). biodb.INFO [2025-03-19 18:27:22.634][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:22.635][biodb::testThat] biodb.INFO [2025-03-19 18:27:22.645][biodb::testThat] biodb.INFO [2025-03-19 18:27:22.646][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. "). biodb.INFO [2025-03-19 18:27:22.646][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:22.646][biodb::testThat] biodb.INFO [2025-03-19 18:27:22.649][biodb::testThat] biodb.INFO [2025-03-19 18:27:22.649][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. "). biodb.INFO [2025-03-19 18:27:22.649][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:22.650][biodb::testThat] biodb.DEBUG[2025-03-19 18:27:22.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:22.651][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:22.652][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:22.652][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:23.078][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:23.705][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:23.706][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content" biodb.TRACE[2025-03-19 18:27:23.708][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request" biodb.TRACE[2025-03-19 18:27:23.712][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:23.713][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:23.713][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:23.713][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:23.713][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:23.714][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:23.714][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:23.714][ef$get] fields variable is a list. biodb.INFO [2025-03-19 18:27:23.715][biodb::testThat] biodb.INFO [2025-03-19 18:27:23.715][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. "). biodb.INFO [2025-03-19 18:27:23.715][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:23.715][biodb::testThat] biodb.ERROR[2025-03-19 18:27:23.719][conn$annotateMzValues] No column named "mz" was found inside data frame. biodb.ERROR[2025-03-19 18:27:23.725][ef$checkIsDefined] Field(s) "foo" is/are not defined. biodb.INFO [2025-03-19 18:27:23.729][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-03-19 18:27:23.729][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2025-03-19 18:27:23.729][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-03-19 18:27:23.730][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-03-19 18:27:23.730][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.730][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.731][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-03-19 18:27:23.734][biodb::testContext] biodb.INFO [2025-03-19 18:27:23.734][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:27:23.735][biodb::testContext] Test context - Test conversions biodb.INFO [2025-03-19 18:27:23.735][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:27:23.735][biodb::testContext] biodb.INFO [2025-03-19 18:27:23.736][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:27:23.736][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-03-19 18:27:23.738][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:23.738][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-03-19 18:27:23.738][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-03-19 18:27:23.738][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.739][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[2025-03-19 18:27:23.739][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-03-19 18:27:23.739][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-03-19 18:27:23.740][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.740][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-03-19 18:27:23.740][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-03-19 18:27:23.741][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.741][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-03-19 18:27:23.742][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-03-19 18:27:23.742][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-03-19 18:27:23.742][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.743][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-03-19 18:27:23.743][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-03-19 18:27:23.743][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-03-19 18:27:23.744][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.744][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[2025-03-19 18:27:23.744][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-03-19 18:27:23.744][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-03-19 18:27:23.745][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.745][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-03-19 18:27:23.746][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-03-19 18:27:23.746][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-03-19 18:27:23.746][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.747][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-03-19 18:27:23.747][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-03-19 18:27:23.747][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.748][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-03-19 18:27:23.748][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-03-19 18:27:23.749][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-03-19 18:27:23.749][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.749][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[2025-03-19 18:27:23.749][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:27:23.750][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-03-19 18:27:23.750][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-03-19 18:27:23.750][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-03-19 18:27:23.750][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-03-19 18:27:23.751][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-03-19 18:27:23.751][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.752][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-03-19 18:27:23.752][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-03-19 18:27:23.752][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.753][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-03-19 18:27:23.753][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-03-19 18:27:23.753][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.754][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-03-19 18:27:23.754][self$set] Set key offline to FALSE. biodb.DEBUG[2025-03-19 18:27:23.754][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.755][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-03-19 18:27:23.755][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-03-19 18:27:23.755][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.756][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-03-19 18:27:23.756][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-03-19 18:27:23.756][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.757][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:27:23.757][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-03-19 18:27:23.762][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-03-19 18:27:23.763][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.764][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-03-19 18:27:23.764][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-03-19 18:27:23.764][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-03-19 18:27:23.764][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.765][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[2025-03-19 18:27:23.765][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-03-19 18:27:23.766][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.766][self$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[2025-03-19 18:27:23.766][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.766][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:23.767][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.767][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:23.767][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.767][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:23.768][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:27:23.768][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:23.768][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.769][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-03-19 18:27:23.769][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:23.769][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.769][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.770][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:23.770][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:23.770][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:23.770][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:27:23.770][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:27:23.770][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:23.770][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.771][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:23.771][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.771][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:23.772][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.772][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:23.772][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:23.772][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.773][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.773][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-03-19 18:27:23.773][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.774][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:27:23.774][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.774][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:23.774][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:23.775][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:23.775][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:27:23.776][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:23.776][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.776][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-03-19 18:27:23.776][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:23.777][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.777][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.777][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:23.777][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:23.777][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:23.777][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:27:23.777][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:27:23.778][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:23.778][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.778][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:23.778][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.779][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:23.779][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.779][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:23.780][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:23.780][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.780][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.780][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-03-19 18:27:23.781][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.781][self$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[2025-03-19 18:27:23.782][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.782][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:23.782][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:23.783][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.783][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:23.783][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:27:23.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:23.784][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.784][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-03-19 18:27:23.784][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:23.784][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.785][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.785][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.785][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:23.785][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.786][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:23.786][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.787][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:23.787][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.787][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:23.787][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:23.788][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.788][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.788][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-03-19 18:27:23.789][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.789][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:27:23.789][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.789][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:23.790][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.790][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:23.790][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.790][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:23.791][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:27:23.791][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:23.791][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.791][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-03-19 18:27:23.792][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:23.792][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.792][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.792][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.793][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:23.793][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.793][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:23.796][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.797][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.798][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:23.798][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.798][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:23.798][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:23.799][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.799][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:23.799][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:23.799][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.800][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.801][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.802][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.803][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.804][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.805][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.806][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.807][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.809][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.810][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.811][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.812][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.813][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.814][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.815][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.816][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[2025-03-19 18:27:23.816][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.817][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.819][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-03-19 18:27:23.819][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-03-19 18:27:23.819][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-03-19 18:27:23.820][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-03-19 18:27:23.820][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:27:23.821][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-03-19 18:27:23.821][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-03-19 18:27:23.821][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-03-19 18:27:23.822][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-03-19 18:27:23.822][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-03-19 18:27:23.822][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:27:23.823][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-03-19 18:27:23.823][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-03-19 18:27:23.824][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-03-19 18:27:23.824][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-03-19 18:27:23.824][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-03-19 18:27:23.825][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-03-19 18:27:23.825][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-03-19 18:27:23.825][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:27:23.826][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-03-19 18:27:23.826][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-03-19 18:27:23.827][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-03-19 18:27:23.827][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-03-19 18:27:23.827][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-03-19 18:27:23.828][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-03-19 18:27:23.828][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-03-19 18:27:23.828][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-03-19 18:27:23.829][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-03-19 18:27:23.829][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-03-19 18:27:23.829][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-03-19 18:27:23.830][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-03-19 18:27:23.830][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-03-19 18:27:23.831][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-03-19 18:27:23.831][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-03-19 18:27:23.831][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-03-19 18:27:23.832][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-03-19 18:27:23.832][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-03-19 18:27:23.832][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-03-19 18:27:23.833][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-03-19 18:27:23.833][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-03-19 18:27:23.833][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-03-19 18:27:23.834][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-03-19 18:27:23.834][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-03-19 18:27:23.835][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-03-19 18:27:23.835][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-03-19 18:27:23.835][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-03-19 18:27:23.836][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-03-19 18:27:23.836][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-03-19 18:27:23.836][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-03-19 18:27:23.837][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-03-19 18:27:23.837][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-03-19 18:27:23.837][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-03-19 18:27:23.838][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-03-19 18:27:23.838][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-03-19 18:27:23.838][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-03-19 18:27:23.839][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-03-19 18:27:23.839][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-03-19 18:27:23.839][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-03-19 18:27:23.840][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-03-19 18:27:23.840][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-03-19 18:27:23.840][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-03-19 18:27:23.841][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-03-19 18:27:23.841][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-03-19 18:27:23.841][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-03-19 18:27:23.842][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-03-19 18:27:23.842][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-03-19 18:27:23.843][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:27:23.843][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:27:23.843][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-03-19 18:27:23.844][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-03-19 18:27:23.844][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-03-19 18:27:23.844][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-03-19 18:27:23.845][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-03-19 18:27:23.845][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-03-19 18:27:23.845][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-03-19 18:27:23.846][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-03-19 18:27:23.846][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-03-19 18:27:23.846][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-03-19 18:27:23.847][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-03-19 18:27:23.847][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-03-19 18:27:23.847][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-03-19 18:27:23.848][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-03-19 18:27:23.848][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-03-19 18:27:23.848][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-03-19 18:27:23.849][initialize] This is biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:27:23.849][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:23.850][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.850][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.850][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.852][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[2025-03-19 18:27:23.852][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.853][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.855][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.856][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.858][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[2025-03-19 18:27:23.858][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.859][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.861][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.862][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.864][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.865][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.866][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.868][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.869][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.870][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[2025-03-19 18:27:23.871][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.872][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.874][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:23.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:23.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:23.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:23.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:23.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:23.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:23.876][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml". biodb.DEBUG[2025-03-19 18:27:23.876][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-03-19 18:27:23.877][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.877][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-03-19 18:27:23.877][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.877][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:23.878][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:23.878][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.879][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-03-19 18:27:23.879][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-03-19 18:27:23.879][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:23.879][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-03-19 18:27:23.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-03-19 18:27:23.883][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-03-19 18:27:23.883][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:23.883][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:23.883][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:23.884][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-03-19 18:27:23.884][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.884][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:23.885][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:23.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:23.885][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:23.885][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:23.885][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-03-19 18:27:23.886][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:23.886][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:23.886][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:23.886][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-03-19 18:27:23.886][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-03-19 18:27:23.887][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:27:23.887][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:27:23.888][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-03-19 18:27:23.888][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:27:23.888][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:27:23.889][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:27:23.890][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-03-19 18:27:23.890][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2025-03-19 18:27:23.890][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2025-03-19 18:27:23.891][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2025-03-19 18:27:23.891][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:27:23.891][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:27:23.892][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2025-03-19 18:27:23.892][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-03-19 18:27:23.892][biodb::testThat] biodb.INFO [2025-03-19 18:27:23.893][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. "). biodb.INFO [2025-03-19 18:27:23.893][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:23.893][biodb::testThat] biodb.DEBUG[2025-03-19 18:27:23.894][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2025-03-19 18:27:23.895][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:23.896][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:23.896][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.TRACE[2025-03-19 18:27:24.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl). biodb.DEBUG[2025-03-19 18:27:24.817][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:24.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content" biodb.TRACE[2025-03-19 18:27:24.819][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request" biodb.DEBUG[2025-03-19 18:27:24.820][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:24.821][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:24.821][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:24.822][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:25.181][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:25.569][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:25.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content" biodb.TRACE[2025-03-19 18:27:25.572][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request" biodb.DEBUG[2025-03-19 18:27:25.572][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:25.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:25.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:25.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:25.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:25.576][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:25.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:25.576][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:25.577][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:25.578][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:25.578][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:25.932][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:26.291][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:26.292][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content" biodb.TRACE[2025-03-19 18:27:26.293][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request" biodb.DEBUG[2025-03-19 18:27:26.294][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:26.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:26.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:26.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:26.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:26.297][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:26.297][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[2025-03-19 18:27:26.303][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:26.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:26.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:26.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:26.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:26.305][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:26.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:26.307][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:26.308][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:26.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3". biodb.TRACE[2025-03-19 18:27:26.309][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:26.309][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content". biodb.DEBUG[2025-03-19 18:27:26.310][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:26.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:26.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:26.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:26.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:26.312][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:26.313][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[2025-03-19 18:27:26.313][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:26.314][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:26.314][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744". biodb.TRACE[2025-03-19 18:27:26.315][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:26.315][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content". biodb.DEBUG[2025-03-19 18:27:26.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:26.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:26.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:26.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:26.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:26.318][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:26.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:26.319][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:26.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:26.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:26.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:26.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:26.321][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:26.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:26.323][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:26.324][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:26.324][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3". biodb.TRACE[2025-03-19 18:27:26.325][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:26.325][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content". biodb.DEBUG[2025-03-19 18:27:26.325][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:26.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:26.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:26.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:26.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:26.328][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:26.328][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[2025-03-19 18:27:26.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:26.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:26.330][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744". biodb.TRACE[2025-03-19 18:27:26.331][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:26.331][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content". biodb.DEBUG[2025-03-19 18:27:26.332][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:26.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:26.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:26.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:26.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:26.334][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:26.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:26.335][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:26.336][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:26.336][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:26.337][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:26.704][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:27.066][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:27.067][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content" biodb.TRACE[2025-03-19 18:27:27.068][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request" biodb.DEBUG[2025-03-19 18:27:27.069][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:27.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:27.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:27.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:27.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:27.072][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:27.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-03-19 18:27:27.075][biodb::testThat] biodb.INFO [2025-03-19 18:27:27.075][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. "). biodb.INFO [2025-03-19 18:27:27.076][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:27.076][biodb::testThat] biodb.DEBUG[2025-03-19 18:27:27.077][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:27.078][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:27.078][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:27.079][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:27.441][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:27.796][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:27.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content" biodb.TRACE[2025-03-19 18:27:27.799][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request" biodb.DEBUG[2025-03-19 18:27:27.800][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:27.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:27.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:27.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:27.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:27.803][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:27.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:27.804][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:27.805][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:27.806][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:27.806][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:28.165][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:28.569][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:28.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content" biodb.TRACE[2025-03-19 18:27:28.572][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request" biodb.DEBUG[2025-03-19 18:27:28.573][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:28.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.576][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-03-19 18:27:28.578][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-03-19 18:27:28.578][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2025-03-19 18:27:28.578][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-03-19 18:27:28.579][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-03-19 18:27:28.579][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.579][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.580][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-03-19 18:27:28.581][biodb::testContext] biodb.INFO [2025-03-19 18:27:28.582][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:27:28.582][biodb::testContext] Test context - Test web services biodb.INFO [2025-03-19 18:27:28.582][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:27:28.582][biodb::testContext] biodb.INFO [2025-03-19 18:27:28.591][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:27:28.592][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-03-19 18:27:28.593][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:28.594][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-03-19 18:27:28.594][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-03-19 18:27:28.594][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.595][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[2025-03-19 18:27:28.595][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-03-19 18:27:28.595][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-03-19 18:27:28.596][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.596][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-03-19 18:27:28.597][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-03-19 18:27:28.597][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.597][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[2025-03-19 18:27:28.597][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-03-19 18:27:28.598][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-03-19 18:27:28.598][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-03-19 18:27:28.598][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.599][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-03-19 18:27:28.599][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-03-19 18:27:28.599][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-03-19 18:27:28.600][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.600][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.DEBUG[2025-03-19 18:27:28.600][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-03-19 18:27:28.601][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-03-19 18:27:28.601][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.601][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-03-19 18:27:28.602][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-03-19 18:27:28.602][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-03-19 18:27:28.602][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.603][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[2025-03-19 18:27:28.603][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-03-19 18:27:28.603][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-03-19 18:27:28.603][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.604][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-03-19 18:27:28.604][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-03-19 18:27:28.605][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-03-19 18:27:28.605][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.605][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:27:28.606][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-03-19 18:27:28.606][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-03-19 18:27:28.606][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-03-19 18:27:28.606][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-03-19 18:27:28.607][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-03-19 18:27:28.607][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.608][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-03-19 18:27:28.608][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-03-19 18:27:28.608][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.609][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-03-19 18:27:28.609][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-03-19 18:27:28.609][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.610][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-03-19 18:27:28.610][self$set] Set key offline to FALSE. biodb.DEBUG[2025-03-19 18:27:28.611][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.611][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-03-19 18:27:28.612][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-03-19 18:27:28.612][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.612][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-03-19 18:27:28.613][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-03-19 18:27:28.613][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.614][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:27:28.614][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-03-19 18:27:28.620][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-03-19 18:27:28.620][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.621][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-03-19 18:27:28.622][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-03-19 18:27:28.622][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-03-19 18:27:28.622][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.623][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[2025-03-19 18:27:28.623][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-03-19 18:27:28.623][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.624][self$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[2025-03-19 18:27:28.624][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.624][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:28.625][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.625][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:28.625][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.625][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:28.626][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:27:28.626][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:28.626][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.626][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:27:28.627][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:27:28.628][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:28.628][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.628][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:28.629][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.629][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:28.629][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.630][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:28.630][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:28.630][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.630][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.631][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-03-19 18:27:28.631][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.632][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:27:28.632][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.632][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:28.632][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.633][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:28.633][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.633][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:28.633][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:27:28.634][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:28.634][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.634][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-03-19 18:27:28.634][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:27:28.635][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:28.636][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.636][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:28.636][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.637][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:28.637][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.637][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:28.638][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:28.638][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.638][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.638][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-03-19 18:27:28.639][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.639][self$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[2025-03-19 18:27:28.639][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.640][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:28.640][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.640][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:28.640][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:28.641][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:27:28.641][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:28.641][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.642][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-03-19 18:27:28.642][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:28.642][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.642][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.643][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.643][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:28.643][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.644][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:28.644][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.644][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:28.645][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.645][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:28.645][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:28.645][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.646][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.646][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-03-19 18:27:28.646][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.647][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:27:28.647][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.647][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:28.647][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.648][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:28.648][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:28.648][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:27:28.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:28.649][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.649][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-03-19 18:27:28.649][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:28.650][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.650][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.650][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.650][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:28.651][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.651][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:28.651][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.652][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:28.652][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.652][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:28.653][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:28.653][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.653][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:28.653][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:28.654][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.654][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.655][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.DEBUG[2025-03-19 18:27:28.655][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.656][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.657][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.659][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.660][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.661][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[2025-03-19 18:27:28.661][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.662][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[2025-03-19 18:27:28.662][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.663][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.664][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.665][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.666][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.667][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.668][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.670][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.670][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[2025-03-19 18:27:28.671][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.672][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.673][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-03-19 18:27:28.673][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-03-19 18:27:28.674][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-03-19 18:27:28.674][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-03-19 18:27:28.675][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:27:28.675][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-03-19 18:27:28.675][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-03-19 18:27:28.676][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-03-19 18:27:28.676][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-03-19 18:27:28.676][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-03-19 18:27:28.677][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:27:28.677][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-03-19 18:27:28.678][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-03-19 18:27:28.678][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-03-19 18:27:28.678][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-03-19 18:27:28.679][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-03-19 18:27:28.679][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-03-19 18:27:28.679][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-03-19 18:27:28.680][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:27:28.680][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-03-19 18:27:28.680][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-03-19 18:27:28.681][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-03-19 18:27:28.681][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-03-19 18:27:28.682][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-03-19 18:27:28.682][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-03-19 18:27:28.682][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-03-19 18:27:28.683][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-03-19 18:27:28.683][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-03-19 18:27:28.683][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-03-19 18:27:28.687][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-03-19 18:27:28.687][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-03-19 18:27:28.687][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-03-19 18:27:28.688][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-03-19 18:27:28.688][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-03-19 18:27:28.689][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-03-19 18:27:28.689][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-03-19 18:27:28.689][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-03-19 18:27:28.690][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-03-19 18:27:28.690][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-03-19 18:27:28.690][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-03-19 18:27:28.691][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-03-19 18:27:28.691][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-03-19 18:27:28.691][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-03-19 18:27:28.692][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-03-19 18:27:28.692][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-03-19 18:27:28.693][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-03-19 18:27:28.693][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-03-19 18:27:28.693][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-03-19 18:27:28.694][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-03-19 18:27:28.694][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-03-19 18:27:28.694][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-03-19 18:27:28.695][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-03-19 18:27:28.695][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-03-19 18:27:28.695][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-03-19 18:27:28.696][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-03-19 18:27:28.696][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-03-19 18:27:28.697][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-03-19 18:27:28.697][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-03-19 18:27:28.697][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-03-19 18:27:28.698][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-03-19 18:27:28.698][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-03-19 18:27:28.698][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-03-19 18:27:28.699][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-03-19 18:27:28.699][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-03-19 18:27:28.700][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-03-19 18:27:28.700][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-03-19 18:27:28.701][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:27:28.701][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:27:28.701][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-03-19 18:27:28.702][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-03-19 18:27:28.702][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-03-19 18:27:28.702][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-03-19 18:27:28.703][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-03-19 18:27:28.703][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-03-19 18:27:28.704][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-03-19 18:27:28.704][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-03-19 18:27:28.704][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-03-19 18:27:28.705][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-03-19 18:27:28.705][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-03-19 18:27:28.705][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-03-19 18:27:28.706][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-03-19 18:27:28.706][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-03-19 18:27:28.706][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-03-19 18:27:28.707][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-03-19 18:27:28.707][initialize] This is biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:27:28.708][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:28.708][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.708][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.709][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.710][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.712][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.714][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.715][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.717][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.718][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.720][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[2025-03-19 18:27:28.720][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.722][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.723][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.725][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.726][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.728][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.729][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[2025-03-19 18:27:28.729][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.731][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.732][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.734][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[2025-03-19 18:27:28.735][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:28.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:28.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:28.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:28.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:28.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:28.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:28.737][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml". biodb.DEBUG[2025-03-19 18:27:28.738][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-03-19 18:27:28.738][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.738][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-03-19 18:27:28.739][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.739][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:28.739][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.739][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:28.740][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.740][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-03-19 18:27:28.740][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-03-19 18:27:28.740][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-03-19 18:27:28.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-03-19 18:27:28.742][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-03-19 18:27:28.742][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:28.742][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:28.742][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:28.742][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-03-19 18:27:28.743][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.743][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:28.743][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:28.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:28.744][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:28.744][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:28.744][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-03-19 18:27:28.744][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:28.744][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:28.745][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:28.745][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-03-19 18:27:28.745][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-03-19 18:27:28.745][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:27:28.746][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:27:28.746][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-03-19 18:27:28.747][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:27:28.747][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:27:28.747][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:27:28.748][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-03-19 18:27:28.749][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2025-03-19 18:27:28.749][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2025-03-19 18:27:28.749][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2025-03-19 18:27:28.750][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:27:28.750][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:27:28.750][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2025-03-19 18:27:28.750][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-03-19 18:27:28.751][biodb::testThat] biodb.INFO [2025-03-19 18:27:28.751][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. "). biodb.INFO [2025-03-19 18:27:28.751][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:28.752][biodb::testThat] biodb.DEBUG[2025-03-19 18:27:28.753][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2025-03-19 18:27:28.754][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:28.754][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2025-03-19 18:27:28.755][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:28.755][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2025-03-19 18:27:28.756][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:28.757][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:28.757][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:28.758][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL". biodb.TRACE[2025-03-19 18:27:29.114][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2025-03-19 18:27:29.469][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:29.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content" biodb.TRACE[2025-03-19 18:27:29.471][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request" biodb.INFO [2025-03-19 18:27:29.474][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-03-19 18:27:29.475][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2025-03-19 18:27:29.475][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-03-19 18:27:29.475][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-03-19 18:27:29.475][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.476][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.476][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-03-19 18:27:29.478][biodb::testContext] biodb.INFO [2025-03-19 18:27:29.478][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:27:29.478][biodb::testContext] Test context - Non regression tests biodb.INFO [2025-03-19 18:27:29.479][biodb::testContext] ******************************************************************************** biodb.INFO [2025-03-19 18:27:29.479][biodb::testContext] biodb.INFO [2025-03-19 18:27:29.480][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:27:29.480][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-03-19 18:27:29.482][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:29.482][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-03-19 18:27:29.482][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-03-19 18:27:29.483][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.483][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-03-19 18:27:29.484][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-03-19 18:27:29.484][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.485][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-03-19 18:27:29.485][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-03-19 18:27:29.485][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.486][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-03-19 18:27:29.486][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-03-19 18:27:29.486][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-03-19 18:27:29.487][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.487][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-03-19 18:27:29.488][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-03-19 18:27:29.488][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-03-19 18:27:29.488][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.489][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-03-19 18:27:29.489][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-03-19 18:27:29.489][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.490][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-03-19 18:27:29.490][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-03-19 18:27:29.490][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-03-19 18:27:29.491][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.495][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-03-19 18:27:29.496][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-03-19 18:27:29.496][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.496][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[2025-03-19 18:27:29.497][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-03-19 18:27:29.497][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-03-19 18:27:29.497][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-03-19 18:27:29.497][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.498][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:27:29.498][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-03-19 18:27:29.499][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-03-19 18:27:29.499][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-03-19 18:27:29.499][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-03-19 18:27:29.499][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-03-19 18:27:29.500][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.500][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-03-19 18:27:29.501][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-03-19 18:27:29.501][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.502][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-03-19 18:27:29.502][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-03-19 18:27:29.502][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.503][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.DEBUG[2025-03-19 18:27:29.503][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-03-19 18:27:29.503][self$set] Set key offline to FALSE. biodb.DEBUG[2025-03-19 18:27:29.503][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.504][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-03-19 18:27:29.504][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-03-19 18:27:29.504][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.505][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-03-19 18:27:29.505][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-03-19 18:27:29.506][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.506][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-03-19 18:27:29.507][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-03-19 18:27:29.513][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-03-19 18:27:29.514][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.514][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-03-19 18:27:29.515][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-03-19 18:27:29.515][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-03-19 18:27:29.515][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.516][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-03-19 18:27:29.517][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.517][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-03-19 18:27:29.517][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.517][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:29.518][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.518][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:29.518][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:29.519][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:27:29.519][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:29.519][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.519][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:27:29.520][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:27:29.521][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:29.521][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.521][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:29.522][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.522][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:29.522][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.523][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:29.523][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:29.523][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.523][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.524][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-03-19 18:27:29.524][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.524][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:27:29.525][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.525][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:29.525][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.525][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:29.526][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.526][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:29.526][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:27:29.526][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:29.527][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.527][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-03-19 18:27:29.527][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:29.527][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:29.528][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.529][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:29.529][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.530][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:29.530][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.530][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:29.530][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:29.531][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.531][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.531][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-03-19 18:27:29.532][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.532][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-03-19 18:27:29.532][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.532][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:29.533][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:29.533][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:29.534][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-03-19 18:27:29.534][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:29.534][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.534][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-03-19 18:27:29.535][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:29.535][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.535][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.535][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.536][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:29.536][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.536][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:29.537][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.537][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:29.537][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.538][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:29.538][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:29.538][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.538][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.539][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-03-19 18:27:29.539][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.539][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-03-19 18:27:29.540][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.540][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:29.540][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.540][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:29.541][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.541][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-03-19 18:27:29.541][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-03-19 18:27:29.541][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:29.542][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.542][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-03-19 18:27:29.542][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:29.542][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.543][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.543][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.543][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-03-19 18:27:29.543][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.544][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:29.545][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.545][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:29.546][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.546][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:29.546][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:29.546][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.547][self$setPropertyValue] biodb.DEBUG[2025-03-19 18:27:29.547][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:29.547][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.548][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.549][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.550][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.551][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[2025-03-19 18:27:29.551][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.552][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[2025-03-19 18:27:29.553][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.554][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.555][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.556][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.557][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[2025-03-19 18:27:29.557][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.558][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.DEBUG[2025-03-19 18:27:29.558][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.559][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[2025-03-19 18:27:29.560][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.561][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.562][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.563][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.564][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.565][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[2025-03-19 18:27:29.565][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.566][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.568][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-03-19 18:27:29.568][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-03-19 18:27:29.568][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-03-19 18:27:29.569][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-03-19 18:27:29.569][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:27:29.569][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-03-19 18:27:29.570][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-03-19 18:27:29.570][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-03-19 18:27:29.570][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-03-19 18:27:29.571][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-03-19 18:27:29.571][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:27:29.572][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-03-19 18:27:29.572][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-03-19 18:27:29.572][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-03-19 18:27:29.573][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-03-19 18:27:29.573][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-03-19 18:27:29.573][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-03-19 18:27:29.574][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-03-19 18:27:29.574][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:27:29.574][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-03-19 18:27:29.575][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-03-19 18:27:29.575][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-03-19 18:27:29.575][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-03-19 18:27:29.576][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-03-19 18:27:29.576][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-03-19 18:27:29.577][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-03-19 18:27:29.577][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-03-19 18:27:29.577][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-03-19 18:27:29.578][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-03-19 18:27:29.578][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-03-19 18:27:29.578][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-03-19 18:27:29.579][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-03-19 18:27:29.579][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-03-19 18:27:29.579][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-03-19 18:27:29.580][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-03-19 18:27:29.580][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-03-19 18:27:29.580][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-03-19 18:27:29.581][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-03-19 18:27:29.581][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-03-19 18:27:29.582][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-03-19 18:27:29.582][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-03-19 18:27:29.582][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-03-19 18:27:29.583][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-03-19 18:27:29.583][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-03-19 18:27:29.583][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-03-19 18:27:29.584][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-03-19 18:27:29.584][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-03-19 18:27:29.584][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-03-19 18:27:29.585][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-03-19 18:27:29.585][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-03-19 18:27:29.585][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-03-19 18:27:29.586][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-03-19 18:27:29.586][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-03-19 18:27:29.586][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-03-19 18:27:29.587][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-03-19 18:27:29.590][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-03-19 18:27:29.590][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-03-19 18:27:29.590][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-03-19 18:27:29.591][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-03-19 18:27:29.591][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-03-19 18:27:29.591][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-03-19 18:27:29.592][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-03-19 18:27:29.592][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-03-19 18:27:29.593][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-03-19 18:27:29.593][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-03-19 18:27:29.593][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-03-19 18:27:29.594][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:27:29.594][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:27:29.594][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-03-19 18:27:29.595][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-03-19 18:27:29.595][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-03-19 18:27:29.595][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-03-19 18:27:29.596][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-03-19 18:27:29.596][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-03-19 18:27:29.596][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-03-19 18:27:29.597][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-03-19 18:27:29.597][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-03-19 18:27:29.597][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-03-19 18:27:29.598][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-03-19 18:27:29.598][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-03-19 18:27:29.598][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-03-19 18:27:29.599][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-03-19 18:27:29.599][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-03-19 18:27:29.599][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-03-19 18:27:29.600][initialize] This is biodb version 1.15.0. biodb.DEBUG[2025-03-19 18:27:29.600][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-03-19 18:27:29.601][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.601][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.602][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.603][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[2025-03-19 18:27:29.603][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.605][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.606][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[2025-03-19 18:27:29.606][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.608][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.609][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.611][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.612][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.614][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.615][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[2025-03-19 18:27:29.615][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.617][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.618][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[2025-03-19 18:27:29.618][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.619][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.DEBUG[2025-03-19 18:27:29.620][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.621][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.623][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.624][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[2025-03-19 18:27:29.624][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.626][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-03-19 18:27:29.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.628][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml". biodb.DEBUG[2025-03-19 18:27:29.628][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2025-03-19 18:27:29.629][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.629][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2025-03-19 18:27:29.629][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.629][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-03-19 18:27:29.630][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.630][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-03-19 18:27:29.630][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.630][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2025-03-19 18:27:29.631][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2025-03-19 18:27:29.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-03-19 18:27:29.631][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.631][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-03-19 18:27:29.632][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-03-19 18:27:29.633][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-03-19 18:27:29.633][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.633][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-03-19 18:27:29.634][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-03-19 18:27:29.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-03-19 18:27:29.634][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-03-19 18:27:29.634][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:29.634][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2025-03-19 18:27:29.635][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-03-19 18:27:29.635][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-03-19 18:27:29.635][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-03-19 18:27:29.635][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2025-03-19 18:27:29.635][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2025-03-19 18:27:29.636][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-03-19 18:27:29.636][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-03-19 18:27:29.636][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2025-03-19 18:27:29.637][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-03-19 18:27:29.637][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-03-19 18:27:29.638][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-03-19 18:27:29.639][super$initialize] Initialize connector chebi. biodb.DEBUG[2025-03-19 18:27:29.639][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2025-03-19 18:27:29.639][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2025-03-19 18:27:29.640][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2025-03-19 18:27:29.640][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:27:29.640][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-03-19 18:27:29.641][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2025-03-19 18:27:29.641][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2025-03-19 18:27:29.641][biodb::testThat] biodb.INFO [2025-03-19 18:27:29.641][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. "). biodb.INFO [2025-03-19 18:27:29.642][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-03-19 18:27:29.642][biodb::testThat] biodb.DEBUG[2025-03-19 18:27:29.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2025-03-19 18:27:29.644][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:29.644][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2025-03-19 18:27:29.645][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:29.645][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2025-03-19 18:27:29.646][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2025-03-19 18:27:29.647][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2025-03-19 18:27:29.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e". biodb.TRACE[2025-03-19 18:27:29.648][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2025-03-19 18:27:29.648][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content". biodb.DEBUG[2025-03-19 18:27:29.650][private$loadEntries] Creating entries from ids [1]: "2571". biodb.DEBUG[2025-03-19 18:27:29.650][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2025-03-19 18:27:29.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571". biodb.TRACE[2025-03-19 18:27:29.651][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2025-03-19 18:27:29.652][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2025-03-19 18:27:29.652][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2025-03-19 18:27:29.652][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2025-03-19 18:27:29.652][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2025-03-19 18:27:29.653][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2025-03-19 18:27:29.653][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:29.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:29.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:29.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:29.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:29.656][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:29.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-03-19 18:27:29.657][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571". biodb.DEBUG[2025-03-19 18:27:29.657][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2025-03-19 18:27:29.658][private$doSendRequestLoop] Request body is "". biodb.TRACE[2025-03-19 18:27:29.658][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571". biodb.TRACE[2025-03-19 18:27:30.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571). biodb.DEBUG[2025-03-19 18:27:32.087][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2025-03-19 18:27:32.088][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content" biodb.TRACE[2025-03-19 18:27:32.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request" biodb.TRACE[2025-03-19 18:27:32.090][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml" biodb.DEBUG[2025-03-19 18:27:32.090][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2025-03-19 18:27:32.090][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2025-03-19 18:27:32.091][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2025-03-19 18:27:32.091][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-03-19 18:27:32.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:32.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:32.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:32.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:32.094][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:32.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-03-19 18:27:32.096][ef$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.096][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.096][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.097][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.098][ef$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:32.098][ef$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:32.099][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.099][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.099][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2025-03-19 18:27:32.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2025-03-19 18:27:32.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.100][ef$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:32.101][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:32.101][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.101][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.101][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-03-19 18:27:32.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-03-19 18:27:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.102][ef$get] Asked field names are: inchi. biodb.TRACE[2025-03-19 18:27:32.103][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-03-19 18:27:32.103][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.103][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.104][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-03-19 18:27:32.104][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-03-19 18:27:32.104][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.104][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.105][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:32.105][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:32.105][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.105][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.106][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:32.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2025-03-19 18:27:32.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.107][ef$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:32.107][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:32.107][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.108][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.108][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2025-03-19 18:27:32.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-03-19 18:27:32.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.109][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:32.112][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:32.113][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.113][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:32.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2025-03-19 18:27:32.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.115][ef$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:32.115][ef$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:32.115][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.116][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-03-19 18:27:32.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-03-19 18:27:32.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.117][ef$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:32.117][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:32.118][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.118][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.118][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2025-03-19 18:27:32.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2025-03-19 18:27:32.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.119][ef$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:32.119][ef$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:32.120][ef$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.120][ef$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.120][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2025-03-19 18:27:32.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2025-03-19 18:27:32.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:32.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:32.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:32.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:32.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2025-03-19 18:27:32.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2025-03-19 18:27:32.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-03-19 18:27:32.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-03-19 18:27:32.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-03-19 18:27:32.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-03-19 18:27:32.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-03-19 18:27:32.131][self$createEntryFromContent] Accession numbers: 2571. biodb.INFO [2025-03-19 18:27:32.133][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-03-19 18:27:32.133][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2025-03-19 18:27:32.133][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2025-03-19 18:27:32.134][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-03-19 18:27:32.134][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-03-19 18:27:32.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-03-19 18:27:32.134][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-03-19 18:27:32.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-03-19 18:27:32.135][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-03-19 18:27:32.135][FUN] Functions in observer 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 386 ] > > proc.time() user system elapsed 5.474 0.377 47.120
biodbChebi.Rcheck/biodbChebi-Ex.timings
name | user | system | elapsed | |
ChebiConn | 0.765 | 0.244 | 2.228 | |
ChebiEntry | 0.112 | 0.004 | 0.117 | |